Index: palm/trunk/TUTORIAL/SOURCE/installation.tex
===================================================================
--- palm/trunk/TUTORIAL/SOURCE/installation.tex	(revision 1233)
+++ palm/trunk/TUTORIAL/SOURCE/installation.tex	(revision 1234)
@@ -1,2 +1,3 @@
+% $Id$
 % $Id$
 \input{header_tmp.tex}
@@ -90,25 +91,27 @@
 % Folie 4
 \begin{frame}
-   \frametitle{PALM - Installation Overview}
+   \frametitle{PALM - Installation on a personal Notebook or a CUHK Desktop PC}
    
    \small
    \begin{itemize}
-      \item<1->{Participants of this seminar will install and use PALM in different ways:} 
-      \item<2->{Installation on a \textcolor{green}{local} computer (either a private Linux notebook or the Linux-cluster at IMUK) and run interactively.}
-      \item<3->{Installation on a \textcolor{green}{local}+\textcolor{red}{remote} computer (Linux-cluster at IMUK + HLRN) and run on the \textcolor{red}{remote} computer (at HLRN) in batch mode. This requires the \textcolor{green}{local} computer to have a fixed IP-address (no DHCP).}
-      \item<4->{We will start with installing PALM on a \textcolor{green}{local} computer and running it interactively.}
+      \item<1->{Participants of this seminar can install and use PALM in different ways:} 
+      \item<2->{Installation on a personal notebook.}
+      \item<3->{Installation on a CUHK desktop PC.}
+      %\item<4->{We will start with installing PALM on a \textcolor{green}{local} computer and running it interactively.}
+      \item<4->{The installation instructions can also be found in the PALM online-documentation under\\ \par\medskip
+            \url{http://palm.muk.uni-hannover.de/wiki/doc/install}}
    \end{itemize}
 \end{frame}
 
 % Folie 5
-\begin{frame}
-   \frametitle{PALM - Installation}
-   
-   \begin{itemize}
-      \item<1->{The following slides describe the installation procedure for running PALM on a \textcolor{green}{local} computer and how to verify the installation.}\\ \par\medskip
-      \item<2->{The installation instructions can also be found in the PALM online-documentation under\\ \par\medskip
-            \url{http://palm.muk.uni-hannover.de/wiki/doc/install}}
-   \end{itemize}
-\end{frame}
+% \begin{frame}
+%    \frametitle{PALM - Installation}
+   
+%    \begin{itemize}
+%       \item<1->{The following slides describe the installation procedure for running PALM on a \textcolor{green}{local} computer and how to verify the installation.}\\ \par\medskip
+%       \item<2->{The installation instructions can also be found in the PALM online-documentation under\\ \par\medskip
+%             \url{http://palm.muk.uni-hannover.de/wiki/doc/install}}
+%    \end{itemize}
+% \end{frame}
 
 % Folie 6
@@ -122,5 +125,5 @@
       \item<3->[3.]{A FORTRAN90/95 compiler.}
       \item<4->[4.]{The Message Passing Interface (MPI),  if the parallel version of PALM shall be used.}
-      \item<5->[5.]{On the \textcolor{green}{local} computer, the revision control system subversion (see subversion.tigris.org). This is already included in many Linux distributions (e.g. SuSe). Subversion requires port 3690 to be open for tcp/udp. If there are firewall restrictions concerning this port, the PALM code cannot be accessed. The user needs a permit to access the PALM repository. For getting a permit please contact the PALM group (raasch@muk.uni-hannover.de) and define a username and a password under which you like to access the repository. This username and password also gives you access to advanced features of the online documentation. (trac-server)}
+      \item<5->[5.]{The revision control system subversion (see subversion.tigris.org). This is already included in many Linux distributions (e.g. SuSe). Subversion requires port 3690 to be open for tcp/udp. If there are firewall restrictions concerning this port, the PALM code cannot be accessed. The user needs a permit to access the PALM repository. For getting a permit please contact the PALM group (raasch@muk.uni-hannover.de) and define a username and a password under which you like to access the repository. This username and password also gives you access to advanced features of the online documentation. (trac-server)}
    \end{itemize}
 \end{frame}
@@ -133,6 +136,6 @@
    \footnotesize 
    \begin{itemize}
-      \item<1->[6.]{All participants of this seminar are already permitted to access the repository. Use \dq seminar2012\dq as username and \dq palm2012\dq as password.}
-      \item<2->[7.]{For the installation of the PALM code on the \textcolor{red}{remote} computer (at HLRN), a sufficient virtual memory has to be allocated on the \textcolor{red}{remote} computer. The value of 256 MByte that is set by \texttt{ulimit -S -v 256000} in the users profile under {\tt $\sim$/.profile} is not sufficient.  Please remove this line in your user profile in order to disable the virtual memory limitation.}
+      \item<1->[6.]{All participants of this seminar are already permitted to access the repository.
+                    Use \dq seminar\_cuhk\dq as username and \dq palm2013\dq as password.}
    \end{itemize}
 \end{frame}
@@ -140,32 +143,14 @@
 % Folie 7
 \begin{frame}
-   \frametitle{List of Usernames / Passwords for PALM 2012 Seminar}
-   
-   \begin{tabbing}
-      IP-address of IMUK: \qquad \=inferno.muk.uni-hannover.de (130.75.105.5)\\
-      IP-address of SGI-ICE:   \>hicegate.hlrn.de  (130.75.4.101)
-   \end{tabbing}
-   \tiny
-   \begin{tabular}[c]{|p{2cm}|p{2cm}|p{2cm}|p{2cm}|p{2cm}|} \hline
-      \textbf{Participant} & \textbf{Username on Linux-cluster (IMUK)} & \textbf{Password (IMUK)} & \textbf{Username on SGI-ICE (HLRN)} & \textbf{Password (HLRN)} \\ \hline
-      Lennart BÃ¶ske & boeske & ... & hzkurs01 & @PSR0723 \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline
-                    &        &     &          &          \\ \hline     
-   \end{tabular}
+   \frametitle{Accounts and Passwords for PALM 2013 Seminar}
+   
+   \begin{itemize}
+      \item<1->{On all the CUHK PCs you can log into the account ``student'' with the corresponding password ``fed19pa!m''.} 
+   \end{itemize}
 \end{frame}
 
 % Folie 8
 \begin{frame}
-   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Download on Linux Notebooks}
+   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Download on Linux Notebooks and CUHK PCs}
    
    \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!100, text width=0.2\textwidth, font=\tiny]
@@ -202,8 +187,8 @@
    \par\medskip
    \begin{itemize}
-      \item<5->[2.]{Create a working copy of the newest PALM version (currently 3.8) from the subversion repository: \\ \par\medskip
+      \item<5->[2.]{Create a working copy of the newest PALM version (currently 3.9) from the subversion repository: \\ \par\medskip
          \qquad {\tt cd $\sim$/palm/current\_version} \\ 
          \qquad {\tt svn checkout --username \textless your username\textgreater \textbackslash} \\
-	     \qquad \qquad {\tt svn://130.75.105.7/palm/tags/release-3.8  trunk} } \\ \par\medskip
+	     \qquad \qquad {\tt svn://130.75.105.7/palm/tags/release-3.9  trunk} } \\ \par\medskip
       \uncover<6->{
       \begin{tikzpicture}[auto]
@@ -223,5 +208,5 @@
          \qquad {\tt cd $\sim$/palm/current\_version} \\ 
          \qquad {\tt svn checkout --username \textless your username\textgreater \textbackslash} \\
-	     \qquad \qquad {\tt svn://130.75.105.7/palm/tags/release-3.8  trunk} }\\ \par\medskip  
+	     \qquad \qquad {\tt svn://130.75.105.7/palm/trunk  trunk} }\\ \par\medskip  
       \item<8->[]{Generally, this version may contain bugs and new features may not be documented! \textbf{Anyhow, using the most recent version is recommended for this seminar!}}
    \end{itemize}
@@ -229,61 +214,4 @@
 
 % Folie 9
-\begin{frame}
-   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Download on IMUK-Linux-cluster}
-   
-   \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!100, text width=0.2\textwidth, font=\tiny]
-   \tikzstyle{yellow2} = [rectangle, draw, fill=yellow!100, text width=0.3\textwidth, font=\tiny]
-   \tikzstyle{yellow3} = [rectangle, draw, fill=yellow!100, text width=0.1\textwidth, font=\tiny]
-   \tikzstyle{yellow4} = [rectangle, draw, fill=yellow!100, text width=0.15\textwidth, font=\tiny]
-   \tikzstyle{green1} = [rectangle, draw, fill=green!75!black, text width=0.1\textwidth, font=\tiny]
-   \tikzstyle{line} = [draw, -]
-   
-   \footnotesize
-   \begin{itemize}
-      \item<2->[1.]{Login from the \textcolor{green}{local} desktop or from your notebook using an ssh-client: \\ \par\smallskip
-         \qquad {\tt ssh -X \textless your IMUK-username\textgreater @inferno.muk.uni-hannover.de}\\ \par\smallskip
-      FORTRAN-compiler, MPI- and netCDF-libraries and all other required software are already installed.} 
-   \end{itemize}
-   \begin{columns}[c]
-   \column{0.5\textwidth}
-      \begin{itemize}
-         \item<3->[2.]{Create your working directory \\ \par\medskip
-            \qquad {\tt mkdir -p $\sim$/palm/current\_version}}
-      \end{itemize}
-   \column{0.42\textwidth}
-      \uncover<4->{
-      \begin{tikzpicture}[auto]
-         \node[yellow1] (home) {\$HOME/};
-         \node[yellow1] (palm) [right=0.4cm of home] {palm/};
-         \node[yellow2] (currentv) [right=0.4cm of palm] {current\_version/};
-         
-         \path[line] (home) -- (palm);
-         \path[line] (palm) -- (currentv);
-      \end{tikzpicture}
-      }
-   \end{columns}
-   \par\medskip
-   \begin{itemize}
-      \item<5->[3.]{Check out the most recent PALM version to your working directory: \\ \par\medskip
-         \qquad {\tt cd $\sim$/palm/current\_version} \\ 
-         \qquad {\tt svn checkout --username \textless your username\textgreater \textbackslash} \\
-	     \qquad \qquad {\tt svn://130.75.105.7/palm/trunk  trunk} } \\ \par\medskip
-      \uncover<6->{
-      \begin{tikzpicture}[auto]
-         \hspace{3cm}
-         \node[yellow3] (home) {\$HOME/};
-         \node[yellow3] (palm) [right=0.4cm of home] {palm/};
-         \node[yellow4] (currentv) [right=0.4cm of palm] {current\_version/};
-         \node[green1] (trunk) [right=0.4cm of currentv] {trunk/};
-         
-         \path[line] (home) -- (palm);
-         \path[line] (palm) -- (currentv);
-         \path[line] (currentv) -- (trunk);
-      \end{tikzpicture}
-      }
-   \end{itemize}
-\end{frame}
-
-% Folie 10
 \begin{frame}
    \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Configuration on Linux Notebooks}
@@ -544,5 +472,5 @@
 % Folie 15
 \begin{frame}
-   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Configuration on IMUK-cluster (I)}
+   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Configuration on the CUHK PCs}
    
    \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!100, text width=0.2\textwidth, font=\tiny]
@@ -556,15 +484,13 @@
    \scriptsize
    \begin{itemize}
-      \item<1->[1.]{Login on host inferno:\\ \par\medskip
-         \qquad {\tt ssh -X \textless your IMUK-username\textgreater @130.75.105.5}} \\ \par\medskip
-      \item<2->[2.]{Set environment variables in the respective profile of the userâs default shell, (which is .\textcolor{red}{my}profile, on the IMUK-Linux-cluster): \\ \par\medskip
-          \uncover<3->{\qquad {\tiny \textcolor{red}{Note: .profile / .bashrc have to be located in \$HOME; recommended text editors are e.g. xedit / vi}}} \\ 
+      \item<1->[1.]{Set environment variables in the respective profile of the userâs default shell, (which is .bashrc, on the CUHK PCs): \\ \par\medskip
+          \uncover<2->{\qquad {\tiny \textcolor{red}{Note: .profile / .bashrc have to be located in \$HOME; recommended text editors are e.g. kate / vi}}} \\ 
           \qquad {\tt export PALM\_BIN=\$HOME/palm/current\_version/trunk/SCRIPTS} \\
           \qquad {\tt export PATH=\$PALM\_BIN:\$PATH}}\\ \par\medskip
-      \item<4->[3.]{Restart the shell (e.g. exit and login (via ssh) again). Otherwise settings are not active.}\\ \par\medskip
-      \item<5->[4.]{Create your personal configuration file, needed by {\tt mbuild} and {\tt mrun}: \\ \par\medskip
+      \item<3->[2.]{Restart the shell. Otherwise settings are not active.}\\ \par\medskip
+      \item<4->[3.]{Create your personal configuration file, needed by {\tt mbuild} and {\tt mrun}: \\ \par\medskip
          \qquad {\tt cd ~/palm/current\_version} \\
-         \qquad {\tt cp trunk/SCRIPTS/.mrun.config.imuk\_hlrn .mrun.config} \\ \par\medskip
-         \uncover<6->{
+         \qquad {\tt cp trunk/SCRIPTS/.mrun.config.cuhk .mrun.config} \\ \par\medskip
+         \uncover<5->{
          \begin{tikzpicture}[auto, >=latex']
               \hspace{0.5cm}
@@ -580,5 +506,5 @@
               \path[line] (trunk) -- (scripts);
               
-              \uncover<7->{\draw [->, thick] {(scripts.south) .. controls (8.0,-1.0) and (4.0,-1.0) .. (currentv.south)};}
+              \uncover<6->{\draw [->, thick] {(scripts.south) .. controls (8.0,-1.0) and (4.0,-1.0) .. (currentv.south)};}
               
               \node[label, right=0pt of scripts] (scriptlabelbase2) {};
@@ -592,42 +518,79 @@
 \end{frame}
 
+% Folie 14a
+\begin{frame}
+   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Configuring {\tt .mrun.config} on CUHK PCs}
+   
+   \tikzstyle{box} = [rectangle, draw, text width=0.9\textwidth, font=\tiny]
+   
+   \scriptsize
+   \begin{itemize}
+      \item{The only parameter that has to be changed is the hostname.}
+      \item{You can find out the hostname by running the program ``hostname'' in your terminal.}
+   \end{itemize}
+      \begin{center}
+      \begin{tikzpicture}[auto, node distance=0]      
+         \node[box](box){ 
+            {\tt \# The next line is just an example. Add your own line below or replace this line.} \\
+            {\tt \%host\_identifier  \textcolor{cyan}{<replace with your hostname>} lccuhk} \\
+            {\tt \#} \\
+            {\tt \# The next block contains all informations for compiling the PALM code} \\
+            {\tt \#} \\
+            \begin{tabbing} 
+            {\tt \%tmp\_use\_catalog} \hspace{0.3cm} \={\tt /home/student/tmp} \hspace{4.0cm} \={\tt lccuhk parallel} \\
+            {\tt \%compiler\_name} \>{\tt mpif90} \>{\tt lccuhk parallel} \\
+            {\tt \%compiler\_name\_ser} \>{\tt ifort} \>{\tt lccuhk parallel} \\
+            {\tt \%cpp\_options} \>{\tt -D\_\_mpi2:-DMPI\_REAL=MPI\_DOUBLE\_PRECISION:} \>{\tt lccuhk parallel} \\
+            {\tt } \>{\tt :-DMPI\_2REAL=MPI\_2DOUBLE\_PRECISION:-D\_\_netcdf} \>{\tt } \\
+            {\tt \%netcdf\_inc} \>{\tt -I:/opt/netcdf-3.6.3/include} \>{\tt lccuhk parallel} \\
+            {\tt \%netcdf\_lib} \>{\tt -L/opt/netcdf-3.6.3/lib:-lnetcdf} \>{\tt lccuhk parallel} \\
+            {\tt \%fopts} \>{\tt -xS:-cpp:-openmp:-r8:-nbs:-convert:little\_endian:} \>{\tt lccuhk parallel} \\
+            {\tt } \>{\tt -I:/opt/mpich2/include} \>{\tt } \\
+            {\tt \%lopts} \>{\tt -xS:-cpp:-openmp:-r8:-nbs:-Vaxlib:} \>{\tt lccuhk parallel} \\
+            {\tt } \>{\tt -L/opt/mpich2/lib} \>{\tt } \\
+            {\tt \%remote\_username} \>{\tt student} \>{\tt lccuhk parallel}
+            \end{tabbing}};
+      \end{tikzpicture}
+      \end{center}
+\end{frame}
+
 % Folie 16
-\begin{frame}
-   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Configuration on IMUK-cluster (II)}
-   
-   \tikzstyle{box} = [rectangle, draw, text width=0.8\textwidth, font=\tiny]
-   
-   \small
-   \begin{itemize}
-      \item<1->[5.]{Edit the configuration file and replace the string {\tt<replace by your IMUK username>}  by your IMUK username and uncomment the respective lines:\\ \par\medskip
-         \qquad {\tt vi .mrun.config}} \\ \par\medskip
-      \begin{itemize}
-      \item<1->{Old: \\
-   \begin{center}
-   \begin{tikzpicture}[auto, node distance=0]      
-      \node[box](box){ 
-         .\\.\\
-         {\tt \# The next block contains all informations for compiling the PALM code}\\ {\tt\#} \\.\\.\\
-         \begin{tabbing} 
-         {\tt \#\%remote\_username} \hspace{0.2cm}  \={\tt \textcolor{blue}{<replace by your IMUK username>}} \hspace{1.6cm} \={\tt lcmuk parallel} \\
-         {\tt \#\%tmp\_use\_catalog} \>{\tt /localdata/\textcolor{blue}{<replace by your IMUK username>}} \>{\tt lcmuk parallel}
-         \end{tabbing}};
-   \end{tikzpicture}
-   \end{center}
-   }
-   \item<2->{New: \\
-   \begin{center}
-   \begin{tikzpicture}[auto, node distance=0]      
-      \node[box](box){
-         \begin{tabbing}
-         {\tt \%remote\_username} \hspace{0.2cm}  \={\tt \textcolor{blue}{your\_name}} \hspace{4.1cm} \={\tt lcmuk parallel} \\
-         {\tt \%tmp\_use\_catalog} \>{\tt /localdata/\textcolor{blue}{your\_name}} \>{\tt lcmuk parallel}
-         \end{tabbing}};
-   \end{tikzpicture}
-   \end{center}
-   }
-      \end{itemize}
-   \end{itemize}
-\end{frame}
+% \begin{frame}
+%     \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Configuration on CUHK PCs (II)}
+   
+%    \tikzstyle{box} = [rectangle, draw, text width=0.8\textwidth, font=\tiny]
+   
+%    \small
+%    \begin{itemize}
+%       \item<1->[5.]{Edit the configuration file and replace the string {\tt<replace by your IMUK username>}  by your IMUK username and uncomment the respective lines:\\ \par\medskip
+%          \qquad {\tt vi .mrun.config}} \\ \par\medskip
+%       \begin{itemize}
+%       \item<1->{Old: \\
+%    \begin{center}
+%    \begin{tikzpicture}[auto, node distance=0]      
+%       \node[box](box){ 
+%          .\\.\\
+%          {\tt \# The next block contains all informations for compiling the PALM code}\\ {\tt\#} \\.\\.\\
+%          \begin{tabbing} 
+%          {\tt \#\%remote\_username} \hspace{0.2cm}  \={\tt \textcolor{blue}{<replace by your IMUK username>}} \hspace{1.6cm} \={\tt lcmuk parallel} \\
+%          {\tt \#\%tmp\_use\_catalog} \>{\tt /localdata/\textcolor{blue}{<replace by your IMUK username>}} \>{\tt lcmuk parallel}
+%          \end{tabbing}};
+%    \end{tikzpicture}
+%    \end{center}
+%    }
+%    \item<2->{New: \\
+%    \begin{center}
+%    \begin{tikzpicture}[auto, node distance=0]      
+%       \node[box](box){
+%          \begin{tabbing}
+%          {\tt \%remote\_username} \hspace{0.2cm}  \={\tt \textcolor{blue}{your\_name}} \hspace{4.1cm} \={\tt lcmuk parallel} \\
+%          {\tt \%tmp\_use\_catalog} \>{\tt /localdata/\textcolor{blue}{your\_name}} \>{\tt lcmuk parallel}
+%          \end{tabbing}};
+%    \end{tikzpicture}
+%    \end{center}
+%    }
+%       \end{itemize}
+%    \end{itemize}
+% \end{frame}
 
 % Folie 17
@@ -800,5 +763,5 @@
 % Folie 20
 \begin{frame}
-   \frametitle{Checking the PALM Installation (I)}
+   \frametitle{Checking the PALM Installation (I) \\ on the \textcolor{green}{local} Computer}
    
    \tikzstyle{blanc} = [rectangle, text width=0\textwidth, font=\scriptsize]
@@ -866,7 +829,7 @@
    Now the job can be run and results can be compared with the reference file
    \begin{itemize}
-      \item<2->[1.]{If {\tt mpich2} is used (e.g. on the IMUK-cluster), the MPI-daemon has to be started as a background process: \\ \par\medskip
-         \qquad {\tt mpd \&} } 
-      \item<3->[2.]{Create and start the (interactive) test run using {\tt mrun}: \\ \par\medskip
+%       \item<2->[1.]{If {\tt mpich2} is used (e.g. on the IMUK-cluster), the MPI-daemon has to be started as a background process: \\ \par\medskip
+%          \qquad {\tt mpd \&} } 
+      \item<2->{Create and start the (interactive) test run using {\tt mrun}: \\ \par\medskip
          \qquad {\tt mrun -d example\_cbl -K parallel -X2 -T2 -r \dq d3\# ts\#\dq} \\ \par\bigskip
       Confirm the terminal query with \dq y\dq. Messages about the progress of execution will be displayed on the terminal and should end (after about 30 s) with \\ \par\medskip
@@ -878,5 +841,5 @@
 % Folie 22
 \begin{frame}
-   \frametitle{Checking the PALM Installation (III)}
+   \frametitle{Checking the PALM Installation (III) \\ on the \textcolor{green}{local} Computer}
    
    \tikzstyle{blanc} = [rectangle, text width=0\textwidth, font=\scriptsize]
@@ -932,21 +895,20 @@
 % Folie 23
 \begin{frame}
-  \frametitle{Installing PALM on IMUKâs inferno \\ Step by Step Instructions (I)}
+  \frametitle{Installing PALM on CUHK PCs \\ Step by Step Instructions (I)}
   
   \footnotesize
   \begin{itemize}
-     \item<2->[1.]{Login on the IMUK-system using the NX-client or an ssh-client:\\ \par\medskip
-        \qquad {\tt ssh -X \textless your IMUK-username\textgreater @130.75.105.5} \\ \par\medskip
-     FORTRAN-compiler, MPI- and netCDF-libraries and all other required software are already installed.}
+     \item<2->[1.]{Log into the CUHK PC using the ``student'' account \\
+                   and the password ``fed19pa!m''}
+     FORTRAN-compiler, MPI- and netCDF-libraries and all other required software are already installed.
      \item<3->[2.]{Download the PALM package by using subversion: \\ \par\medskip
         \qquad {\tt mkdir -p $\sim$/palm/current\_version} \\
         \qquad {\tt cd $\sim$/palm/current\_version} \\
-        \qquad {\tt svn checkout --username \textless your IMUK-username\textgreater \quad \textbackslash} \\
+        \qquad {\tt svn checkout --username seminar\_cuhk \quad \textbackslash} \\
         \qquad \qquad{\tt svn://130.75.105.7/palm/trunk trunk }} 
      \item<4->[3.]{Set environment variables: \\ \par\medskip
         \qquad {\tt export PALM\_BIN=\$HOME/palm/current\_version/trunk/SCRIPTS} \\
         \qquad {\tt export PATH=\$PALM\_BIN:\$PATH} \\ \par\medskip
-     Set these variables also in file {\tt .myprofile.} or \\ \par\medskip
-        \qquad {\tt cp /home/raasch/.myprofile \qquad \$HOME}}
+     Set these variables also in file {\tt .bashrc.}}
   \end{itemize}
 \end{frame}
@@ -954,16 +916,15 @@
 % Folie 24
 \begin{frame}
-   \frametitle{Installing PALM on IMUKâs inferno \\ Step by Step Instructions (II)}
+   \frametitle{Installing PALM on CUHK PCs \\ Step by Step Instructions (II)}
    
    \footnotesize
    \begin{itemize}
       \item<1->[4.]{A pre-configured configuration file for the IMUK/HLRN system is available: \\ \par\medskip
-         \qquad{\tt cp trunk/SCRIPTS/.mrun.config.imuk\_hlrn .mrun.config}}\\ \par\medskip
-      \item<2->[5.]{Edit this file and replace the string \textless replace by your IMUK username\textgreater \ with your IMUK-username. (Do not forget to uncomment the respective two lines!)} 
-      \item<3->[6.]{Create the utility programs: \\ \par\medskip
-         \qquad {\tt mbuild -u -h lcmuk}}\\ \par\medskip
-      \item<4->[7.]{Pre-compile the PALM code:\\ \par\medskip
-         \qquad{\tt mbuild -h lcmuk}}\\ \par\medskip
-      \item<5->[8.]{Provide the parameter file: \\ \par\medskip
+         \qquad{\tt cp trunk/SCRIPTS/.mrun.config.cuhk .mrun.config}}\\ \par\medskip
+      \item<2->[5.]{Create the utility programs: \\ \par\medskip
+         \qquad {\tt mbuild -u -h lccuhk}}\\ \par\medskip
+      \item<3->[6.]{Pre-compile the PALM code:\\ \par\medskip
+         \qquad{\tt mbuild -h lccuhk}}\\ \par\medskip
+      \item<4->[7.]{Provide the parameter file: \\ \par\medskip
          \qquad{\tt mkdir -p JOBS/example\_cbl/INPUT} \\
          \qquad{\tt cp trunk/INSTALL/example\_cbl\_p3d JOBS/example\_cbl/INPUT}}
@@ -973,11 +934,11 @@
 % Folie 25
 \begin{frame}
-   \frametitle{Installing PALM on IMUKâs inferno \\ Step by Step Instructions (III)}
+   \frametitle{Installing PALM on CUHK PCs \\ Step by Step Instructions (III)}
    
    \footnotesize
    \begin{itemize}
-      \item<1->[9.]{Carry out the test run: \\ \par\medskip
+      \item<1->[8.]{Carry out the test run: \\ \par\medskip
          \qquad{\tt mrun -d example\_cbl -K parallel -X2 -T2 -r \dq d3\#\dq}}
-      \item<2->[10.]{Check results (after job has finished): \\ \par\medskip
+      \item<2->[9.]{Check results (after job has finished): \\ \par\medskip
          \qquad{\tt cd JOBS/example\_cbl/MONITORING} \\
          \qquad{\tt kdiff3 example\_cbl\_rc ../../../trunk/INSTALL/example\_cbl\_rc}}
@@ -985,167 +946,3 @@
 \end{frame}
 
-% Folie 26
-\begin{frame}
-   \frametitle{Installing PALM on a \textcolor{red}{remote} Computer (HLRN) \\ Step by Step Instructions (I)}
-   \footnotesize
-   \begin{itemize}
-      \item<1->[1.]{Create your working directory on the \textcolor{red}{remote} host: \\ \par\medskip
-         \qquad {\tt ssh \textless your HLRN-username\textgreater@hicegate.hlrn.de}\\
-         \qquad {\tt mkdir -p $\sim$/palm/current\_version}}  
-      \item<2->[2.]{Set environment variables on the \textcolor{red}{remote} host: \\ \par\medskip
-         \qquad{\tt export PALM\_BIN=\$HOME/palm/current\_version/trunk/SCRIPTS} \\
-         \qquad{\tt export PATH=\$PALM\_BIN:\$PATH} \\ \par\medskip
-      This has to be done in file {\tt $\sim$/.bashrc} or  in file {\tt $\sim$/.profile}, depending on your default shell. You can get your default shell via command: \\ \par\medskip
-         \qquad{\tt echo \$SHELL}}
-      \item<3->[3.]{Please also remove the line \texttt{ulimit -S -v 256000} in file {\tt $\sim$/.profile} to disable the virtual memory limitation of 256 MByte that is set for your seminar user account.}
-   \end{itemize}
-\end{frame}
-
-% Folie 27
-\begin{frame}
-   \frametitle{Installing PALM on a \textcolor{red}{remote} Computer (HLRN) \\ Step by Step Instructions (II)}
-   \footnotesize
-   \begin{itemize}
-      \item<1->[4.]{On the \textcolor{green}{local} host, edit your configuration file ({\tt .mrun.config}), and replace in the lcsgih-block \textless replace by your HLRN username\textgreater with your HLRN-username.}\\ \par\medskip
-      \item<2->[5.]{Create directory {\tt job\_queue} on the \textcolor{green}{local} and the \textcolor{red}{remote} host:\\ \par\medskip
-         \qquad{\tt mkdir $\sim$/job\_queue}}
-   \end{itemize}
-\end{frame}
-
-% Folie 28
-\begin{frame}
-   \frametitle{Establishing the ssh Public-Key Authentication}
-   
-   \tikzstyle{blue} = [rectangle, draw, align=center, color=green, text width=0.18\textwidth, font=\tiny]
-   \tikzstyle{red} = [rectangle, draw, align=center, color=red, text width=0.18\textwidth, font=\tiny]
-   \tikzstyle{label} = [rectangle, font=\tiny, minimum size=8pt]
-   
-   \footnotesize
-   The PALM-tools (mrun, mbuild) are using ssh/scp for batch jobs on \textcolor{red}{remote} computers and require, that ssh/scp does not prompt for passwords.This can be managed by using the public-key authentication method. \\ \par\medskip
-   Public-key authentication is needed for connections in both directions! \\ \par\medskip
-   \begin{center}
-      \begin{tikzpicture}[auto, >=latex']
-         \coordinate (p0) at (-2.0cm,0.0cm);
-         \coordinate (p1) at (2.0cm,0.0cm);
-         \coordinate (p2) at (-2.0cm,0.2cm);
-         \coordinate (p3) at (2.0cm,0.2cm);
-         \coordinate (p4) at (-2.0cm,-0.2cm);
-         \coordinate (p5) at (2.0cm,-0.2cm);
-         
-         \coordinate (p6) at (0.0cm,0.0cm);
-         
-         \draw[->, thick, color=green] (p2) -- (p3);
-         \draw[<-, thick, color=red] (p4) -- (p5);
-         
-         \node[blue] (green) [left=0.4cm of p0] {
-            local computer\\
-            \textless{IP-local}\textgreater\\
-            OpenSSH
-         };
-         \node[red] (red) [right=0.4cm of p1] {
-            remote computer\\
-            \textless{IP-remote}\textgreater\\
-            OpenSSH
-         };
-         
-         \node[label, above=0.3cm of p6] (labelblue) {{\tt ssh <HLRN-username>@<130.75.4.101>}};
-         \node[label, below=0.3cm of p6] (labelred) {{\tt ssh <HLRN-username>@<130.75.4.101>}};
-      \end{tikzpicture}
-   \end{center}
-   \uncover<2->{Pre-requisites:}\\
-   \begin{itemize}
-      \item<3->[1.]{On the \textcolor{green}{local} system (IMUK, OpenSSH): create .ssh directory (if not existing):\\ \par\medskip
-         \qquad{\tt mkdir $\sim$/.ssh}\\
-         \qquad{\tt chmod go-rwx $\sim$/.ssh}} \par\medskip
-      \item<4->[2.]{On the \textcolor{red}{remote} system (HLRN, OpenSSH): create .ssh directory (if not existing):\\ \par\medskip
-         \qquad{\tt mkdir $\sim$/.ssh}\\
-         \qquad{\tt chmod go-rwx $\sim$/.ssh}}
-   \end{itemize}
-\end{frame}
-
-% Folie 29
-\begin{frame}
-   \frametitle{Enable public-key authentication for connections from the \textcolor{green}{local} system to the \textcolor{red}{remote} system:}
-   
-   \footnotesize
-   On the \textcolor{green}{local} system (inferno.muk.uni-hannover.de, 130.75.105.5):
-   \begin{itemize}
-      \item<2->[1.]{create the key:\\ \par\medskip
-         \qquad{\tt cd $\sim$/.ssh}\\
-         \qquad{\tt ssh-keygen -b 2048 -t dsa}\\
-         \qquad\qquad{\tt \# creates files id\_dsa and id\_dsa.pub}\\
-         \qquad\qquad{\tt \# type <return> when asked for passphrase!!}} \par\medskip
-      \item<3->[2.]{copy the public key to the \textcolor{red}{remote} system:\\ \par\medskip
-         \qquad{\tt scp id\_dsa.pub <HLRN-usern>@130.75.4.101:.ssh/authorized\_keys}}
-   \end{itemize}
-\end{frame}
-
-% Folie 30
-\begin{frame}
-   \frametitle{Enable public-key authentication for connections from the \textcolor{red}{remote} system to the \textcolor{green}{local} system:}
-   
-   \footnotesize
-   On the \textcolor{red}{remote} system (hicegate.hlrn.de, 130.75.4.101):
-   \begin{itemize}
-      \item<2->[1.]{Create the key:\\ \par\medskip
-         \qquad{\tt cd $\sim$/.ssh}\\
-         \qquad{\tt ssh-keygen -t dsa}\\
-         \qquad\qquad{\tt \# creates files id\_dsa and id\_dsa.pub}\\
-         \qquad\qquad{\tt \# type <return> when asked for passphrase!!}} \par\medskip
-      \item<3->[2.]{Copy the public key to the \textcolor{green}{local} system:\\ \par\medskip
-         \qquad{\tt scp id\_dsa.pub <IMUK-usern>@130.75.105.5:.ssh/authorized\_keys}}\\ \par\medskip
-      \item<4->[3.]{Append the public key also to the HLRN authorized\_keys file:\\ \par\medskip
-         \qquad{\tt cat id\_dsa.pub >> authorized\_keys}}
-   \end{itemize}
-\end{frame}
-
-% Folie 31
-\begin{frame}
-   \frametitle{Establishing the ssh Public-Key Authentication}
-   
-   \footnotesize
-   \underline{Final action:}\\ \par\medskip
-   Establish ssh-connection at least one time from the \textcolor{green}{local} host to the \textcolor{red}{remote} host and vice versa.\\ \par\medskip
-   Use IP-adresses (eg. 130.75...) and not the symbolic names (e.g. ...hlrn.de)!\\ \par\medskip
-   After this, {\tt ssh-} and {\tt scp-} calls should not prompt for passwords any more. Please test at least one time from the \textcolor{red}{remote} to the \textcolor{green}{local} host, because the first ssh connection requires a confirmation to be typed from the keyboard!\\ \par\medskip
-   \begin{itemize}
-      \item<2->[1.]{On the \textcolor{green}{local} system (inferno):\\ \par\medskip
-         \qquad{\tt ssh <HLRN-username>@130.75.4.101}} \par\medskip
-      \item<3->[2.]{On the \textcolor{red}{remote} system (hicegate):\\ \par\medskip
-         \qquad{\tt ssh <IMUK-username>@130.75.105.5}}\\
-   \end{itemize}
-\end{frame}
-
-% Folie 32
-\begin{frame}
-   \frametitle{Installing PALM on a \textcolor{red}{remote} Computer (HLRN) \\ Step by Step Instructions (III)}
-   \footnotesize
-   \begin{itemize}
-      \item<1->[5.]{Create the utility programs on the \textcolor{red}{remote} host by executing the following command on the \textcolor{green}{local} host: \\ \par\medskip
-         \qquad{\tt mbuild -u -h lcsgih} \\ \par\medskip
-      This command also copies some shellscripts required to run PALM from the \textcolor{green}{local} host to the directory {\tt $\sim$/palm/current\_version/trunk/SCRIPTS} on the \textcolor{red}{remote} host.} \\ \par\medskip
-      \item<2->[6.]{Pre-compile the PALM code on the \textcolor{red}{remote} host: \\ \par\medskip
-         \qquad{\tt mbuild -h lcsgih}} \\ \par\medskip
-      \item<3->[7.]{Create the temporary working catalog on the \textcolor{red}{remote} host, if it does not exist (this is the directory given for the \textcolor{red}{remote} host by the environment variable {\tt tmp\_user\_catalog} in the configuration file {\tt .mrun.config}):\\ \par\medskip
-         \qquad{\tt mkdir \textless tmp\_user\_catalog\textgreater}}
-   \end{itemize}
-\end{frame}
-
-% Folie 33
-\begin{frame}
-   \frametitle{Installing PALM on a \textcolor{red}{remote} Computer (HLRN) \\ Step by Step Instructions (IV)}
-   \footnotesize
-   \begin{itemize}
-      \item<1->[8.]{Carry out the test run by calling mrun on the \textcolor{green}{local} host:\\ \par\medskip
-         \qquad{\tt mrun -d example\_cbl -h lcsgih -K parallel -X8 -T2 -q testq}\\
-         \qquad{\tt -t 300 -r \dq d3\#\dq}}\\ \par\medskip
-      \item<2->[9.]{After the job has finished on the \textcolor{red}{remote} host, results will be automatically transferred to the \textcolor{green}{local} host. Check the results on the \textcolor{green}{local} host:\\ \par\medskip
-         \qquad{\tt cd JOBS/example\_cbl/MONITORING} \\
-         \qquad{\tt kdiff3 lcsgih\_example\_cbl\_rc}\\
-         \qquad{\tt ../../../trunk/INSTALL/example\_cbl\_rc}}
-   \end{itemize}
-
-\end{frame}
-
-
 \end{document}
Index: palm/trunk/TUTORIAL/SOURCE/program_structure.tex
===================================================================
--- palm/trunk/TUTORIAL/SOURCE/program_structure.tex	(revision 1233)
+++ palm/trunk/TUTORIAL/SOURCE/program_structure.tex	(revision 1234)
@@ -471,5 +471,5 @@
    \tikzstyle{greenLarge} = [rectangle, draw, fill=green!20, text width=0.3\textwidth, minimum size=12pt, font=\tiny]
    \tikzstyle{line} = [draw, -]
-   \tikzstyle{linered} = [draw, color=red, -]
+
    \tikzstyle{Bigwhite} = [rectangle, text width=0.63\textwidth, minimum size=35pt, font=\tiny]
    \tikzstyle{Bigbox} = [rectangle, draw, fill=gray!20, text width=0.65\textwidth, minimum size=33pt, font=\tiny]
@@ -512,5 +512,5 @@
 %            \uncover<1->{\node [yellowLarge, below=0.05cm of prognosticequca] (prognosticequve) {prognostic\_equations\_vector};}
             \uncover<1->{\node [boxinfo, below=-0.025cm of prognosticequve] (Boxinfo) {For details, see \\ PALM Flow Chart (VIII).};}
-            \path<1-> [linered] (boxlinespace.north) -| (prognosticequca.north);
+            \path<1-> [line] (boxlinespace.north) -| (prognosticequca.north);
             \path<1-> [line] (boxlinespace.north) -| (prognosticequve.north);
 %            \uncover<1->{\node [redsmall, above=0.3cm of prognosticequca] (redadv) {standard\\advection};}
@@ -730,7 +730,6 @@
 
       \uncover<1->{\node [Bigbox] (bigbox) {};}
-      \uncover<1->{\node [redsmall, above=-0.23cm of bigbox] (redadv) {standard advection};}
-
-      \uncover<1->{\node [yellow, below=0.1cm of redadv] (calcmeanptprofile) {calc\_mean\_pt\_profile};}
+
+      \uncover<1->{\node [yellow, above=-0.75cm of bigbox] (calcmeanptprofile) {calc\_mean\_pt\_profile};}
 
 %      \uncover<1->{\node [yellowLarge, left=0.5cm of calcmeanptprofile] (prognosticequationsnoopt) {prognostic\_equations\_noopt};}
Index: palm/trunk/TUTORIAL/SOURCE/user_defined_code.tex
===================================================================
--- palm/trunk/TUTORIAL/SOURCE/user_defined_code.tex	(revision 1233)
+++ palm/trunk/TUTORIAL/SOURCE/user_defined_code.tex	(revision 1234)
@@ -306,8 +306,7 @@
       \node[green, right=0.6cm of B, text width=14em] (useractions1) {\textcolor{blue}{user\_actions\_(\textit{'before\_timestep'})}};    
          
-      \node[orange1, below=0.2cm of D] (progeq) {prognostic\_equations};    
-      \node[orange1, below=0.2cm of E] (progeqfast) {prognostic\_equations\_fast};
-      \node[draw, fill=red, text width=4em] at (8.6,-0.8) {\textcolor{white}{standard advection}};
-                
+      \node[orange1, below=0.2cm of D] (progeq) {prognostic\_equations\_vector};    
+      \node[orange1, below=0.2cm of E] (progeqfast) {prognostic\_equations\_cache};
+           
       \node[green, right=0.3cm of progframe, text width=14em] (useractions2) {\textcolor{blue}{user\_actions\_(\textit{'*\_tendency'})}}; 
       
@@ -365,7 +364,7 @@
       \draw[-, thick] (B) -- (useractions1);
       \draw[-, thick] (C) -- (D);
+      \draw[-, thick] (D) -- (E);
+      \draw[->, thick] (E) -- (progeqfast);
       \draw[-, thick] (progeq) -- (D);      
-      \draw[-, thick, color=red] (D) -- (E); 
-      \draw[->, thick, color=red] (E) -- (progeqfast);        
       \draw[-, thick] (progframe) -- (useractions2); 
       \draw[-, thick] (F) -- (lpm);    
