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Changeset 1234 for palm/trunk/TUTORIAL


Ignore:
Timestamp:
Sep 25, 2013 6:17:49 AM (11 years ago)
Author:
kanani
Message:

update of some tutorial presentations

Location:
palm/trunk/TUTORIAL/SOURCE
Files:
3 edited

Legend:

Unmodified
Added
Removed

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

    r1226 r1234  
     1% $Id$
    12% $Id$
    23\input{header_tmp.tex}
    … …  
    9091% Folie 4
    9192\begin{frame}
    92    \frametitle{PALM - Installation Overview}
     93   \frametitle{PALM - Installation on a personal Notebook or a CUHK Desktop PC}
    9394   
    9495   \small
    9596   \begin{itemize}
    96       \item<1->{Participants of this seminar will install and use PALM in different ways:}
    97       \item<2->{Installation on a \textcolor{green}{local} computer (either a private Linux notebook or the Linux-cluster at IMUK) and run interactively.}
    98       \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).}
    99       \item<4->{We will start with installing PALM on a \textcolor{green}{local} computer and running it interactively.}
     97      \item<1->{Participants of this seminar can install and use PALM in different ways:}
     98      \item<2->{Installation on a personal notebook.}
     99      \item<3->{Installation on a CUHK desktop PC.}
     100      %\item<4->{We will start with installing PALM on a \textcolor{green}{local} computer and running it interactively.}
     101      \item<4->{The installation instructions can also be found in the PALM online-documentation under\\ \par\medskip
     102            \url{http://palm.muk.uni-hannover.de/wiki/doc/install}}
    100103   \end{itemize}
    101104\end{frame}
    102105
    103106% Folie 5
    104 \begin{frame}
    105    \frametitle{PALM - Installation}
    106    
    107    \begin{itemize}
    108       \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
    109       \item<2->{The installation instructions can also be found in the PALM online-documentation under\\ \par\medskip
    110             \url{http://palm.muk.uni-hannover.de/wiki/doc/install}}
    111    \end{itemize}
    112 \end{frame}
     107% \begin{frame}
     108%    \frametitle{PALM - Installation}
     109   
     110%    \begin{itemize}
     111%       \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
     112%       \item<2->{The installation instructions can also be found in the PALM online-documentation under\\ \par\medskip
     113%             \url{http://palm.muk.uni-hannover.de/wiki/doc/install}}
     114%    \end{itemize}
     115% \end{frame}
    113116
    114117% Folie 6
    … …  
    122125      \item<3->[3.]{A FORTRAN90/95 compiler.}
    123126      \item<4->[4.]{The Message Passing Interface (MPI),  if the parallel version of PALM shall be used.}
    124       \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)}
     127      \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)}
    125128   \end{itemize}
    126129\end{frame}
    … …  
    133136   \footnotesize
    134137   \begin{itemize}
    135       \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.}
    136       \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.}
     138      \item<1->[6.]{All participants of this seminar are already permitted to access the repository.
     139                    Use \dq seminar\_cuhk\dq as username and \dq palm2013\dq as password.}
    137140   \end{itemize}
    138141\end{frame}
    … …  
    140143% Folie 7
    141144\begin{frame}
    142    \frametitle{List of Usernames / Passwords for PALM 2012 Seminar}
    143    
    144    \begin{tabbing}
    145       IP-address of IMUK: \qquad \=inferno.muk.uni-hannover.de (130.75.105.5)\\
    146       IP-address of SGI-ICE:   \>hicegate.hlrn.de  (130.75.4.101)
    147    \end{tabbing}
    148    \tiny
    149    \begin{tabular}[c]{|p{2cm}|p{2cm}|p{2cm}|p{2cm}|p{2cm}|} \hline
    150       \textbf{Participant} & \textbf{Username on Linux-cluster (IMUK)} & \textbf{Password (IMUK)} & \textbf{Username on SGI-ICE (HLRN)} & \textbf{Password (HLRN)} \\ \hline
    151       Lennart Böske & boeske & ... & hzkurs01 & @PSR0723 \\ \hline
    152                     &        &     &          &          \\ \hline
    153                     &        &     &          &          \\ \hline
    154                     &        &     &          &          \\ \hline
    155                     &        &     &          &          \\ \hline
    156                     &        &     &          &          \\ \hline
    157                     &        &     &          &          \\ \hline
    158                     &        &     &          &          \\ \hline
    159                     &        &     &          &          \\ \hline
    160                     &        &     &          &          \\ \hline
    161                     &        &     &          &          \\ \hline
    162                     &        &     &          &          \\ \hline
    163                     &        &     &          &          \\ \hline     
    164    \end{tabular}
     145   \frametitle{Accounts and Passwords for PALM 2013 Seminar}
     146   
     147   \begin{itemize}
     148      \item<1->{On all the CUHK PCs you can log into the account ``student'' with the corresponding password ``fed19pa!m''.}
     149   \end{itemize}
    165150\end{frame}
    166151
    167152% Folie 8
    168153\begin{frame}
    169    \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Download on Linux Notebooks}
     154   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Download on Linux Notebooks and CUHK PCs}
    170155   
    171156   \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!100, text width=0.2\textwidth, font=\tiny]
    … …  
    202187   \par\medskip
    203188   \begin{itemize}
    204       \item<5->[2.]{Create a working copy of the newest PALM version (currently 3.8) from the subversion repository: \\ \par\medskip
     189      \item<5->[2.]{Create a working copy of the newest PALM version (currently 3.9) from the subversion repository: \\ \par\medskip
    205190         \qquad {\tt cd $\sim$/palm/current\_version} \\
    206191         \qquad {\tt svn checkout --username \textless your username\textgreater \textbackslash} \\
    207              \qquad \qquad {\tt svn://130.75.105.7/palm/tags/release-3.8  trunk} } \\ \par\medskip
     192             \qquad \qquad {\tt svn://130.75.105.7/palm/tags/release-3.9  trunk} } \\ \par\medskip
    208193      \uncover<6->{
    209194      \begin{tikzpicture}[auto]
    … …  
    223208         \qquad {\tt cd $\sim$/palm/current\_version} \\
    224209         \qquad {\tt svn checkout --username \textless your username\textgreater \textbackslash} \\
    225              \qquad \qquad {\tt svn://130.75.105.7/palm/tags/release-3.8  trunk} }\\ \par\medskip 
     210             \qquad \qquad {\tt svn://130.75.105.7/palm/trunk  trunk} }\\ \par\medskip 
    226211      \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!}}
    227212   \end{itemize}
    … …  
    229214
    230215% Folie 9
    231 \begin{frame}
    232    \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Download on IMUK-Linux-cluster}
    233    
    234    \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!100, text width=0.2\textwidth, font=\tiny]
    235    \tikzstyle{yellow2} = [rectangle, draw, fill=yellow!100, text width=0.3\textwidth, font=\tiny]
    236    \tikzstyle{yellow3} = [rectangle, draw, fill=yellow!100, text width=0.1\textwidth, font=\tiny]
    237    \tikzstyle{yellow4} = [rectangle, draw, fill=yellow!100, text width=0.15\textwidth, font=\tiny]
    238    \tikzstyle{green1} = [rectangle, draw, fill=green!75!black, text width=0.1\textwidth, font=\tiny]
    239    \tikzstyle{line} = [draw, -]
    240    
    241    \footnotesize
    242    \begin{itemize}
    243       \item<2->[1.]{Login from the \textcolor{green}{local} desktop or from your notebook using an ssh-client: \\ \par\smallskip
    244          \qquad {\tt ssh -X \textless your IMUK-username\textgreater @inferno.muk.uni-hannover.de}\\ \par\smallskip
    245       FORTRAN-compiler, MPI- and netCDF-libraries and all other required software are already installed.}
    246    \end{itemize}
    247    \begin{columns}[c]
    248    \column{0.5\textwidth}
    249       \begin{itemize}
    250          \item<3->[2.]{Create your working directory \\ \par\medskip
    251             \qquad {\tt mkdir -p $\sim$/palm/current\_version}}
    252       \end{itemize}
    253    \column{0.42\textwidth}
    254       \uncover<4->{
    255       \begin{tikzpicture}[auto]
    256          \node[yellow1] (home) {\$HOME/};
    257          \node[yellow1] (palm) [right=0.4cm of home] {palm/};
    258          \node[yellow2] (currentv) [right=0.4cm of palm] {current\_version/};
    259          
    260          \path[line] (home) -- (palm);
    261          \path[line] (palm) -- (currentv);
    262       \end{tikzpicture}
    263       }
    264    \end{columns}
    265    \par\medskip
    266    \begin{itemize}
    267       \item<5->[3.]{Check out the most recent PALM version to your working directory: \\ \par\medskip
    268          \qquad {\tt cd $\sim$/palm/current\_version} \\
    269          \qquad {\tt svn checkout --username \textless your username\textgreater \textbackslash} \\
    270              \qquad \qquad {\tt svn://130.75.105.7/palm/trunk  trunk} } \\ \par\medskip
    271       \uncover<6->{
    272       \begin{tikzpicture}[auto]
    273          \hspace{3cm}
    274          \node[yellow3] (home) {\$HOME/};
    275          \node[yellow3] (palm) [right=0.4cm of home] {palm/};
    276          \node[yellow4] (currentv) [right=0.4cm of palm] {current\_version/};
    277          \node[green1] (trunk) [right=0.4cm of currentv] {trunk/};
    278          
    279          \path[line] (home) -- (palm);
    280          \path[line] (palm) -- (currentv);
    281          \path[line] (currentv) -- (trunk);
    282       \end{tikzpicture}
    283       }
    284    \end{itemize}
    285 \end{frame}
    286 
    287 % Folie 10
    288216\begin{frame}
    289217   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Configuration on Linux Notebooks}
    … …  
    544472% Folie 15
    545473\begin{frame}
    546    \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Configuration on IMUK-cluster (I)}
     474   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Configuration on the CUHK PCs}
    547475   
    548476   \tikzstyle{yellow1} = [rectangle, draw, fill=yellow!100, text width=0.2\textwidth, font=\tiny]
    … …  
    556484   \scriptsize
    557485   \begin{itemize}
    558       \item<1->[1.]{Login on host inferno:\\ \par\medskip
    559          \qquad {\tt ssh -X \textless your IMUK-username\textgreater @130.75.105.5}} \\ \par\medskip
    560       \item<2->[2.]{Set environment variables in the respective profile of the user‘s default shell, (which is .\textcolor{red}{my}profile, on the IMUK-Linux-cluster): \\ \par\medskip
    561           \uncover<3->{\qquad {\tiny \textcolor{red}{Note: .profile / .bashrc have to be located in \$HOME; recommended text editors are e.g. xedit / vi}}} \\
     486      \item<1->[1.]{Set environment variables in the respective profile of the user‘s default shell, (which is .bashrc, on the CUHK PCs): \\ \par\medskip
     487          \uncover<2->{\qquad {\tiny \textcolor{red}{Note: .profile / .bashrc have to be located in \$HOME; recommended text editors are e.g. kate / vi}}} \\
    562488          \qquad {\tt export PALM\_BIN=\$HOME/palm/current\_version/trunk/SCRIPTS} \\
    563489          \qquad {\tt export PATH=\$PALM\_BIN:\$PATH}}\\ \par\medskip
    564       \item<4->[3.]{Restart the shell (e.g. exit and login (via ssh) again). Otherwise settings are not active.}\\ \par\medskip
    565       \item<5->[4.]{Create your personal configuration file, needed by {\tt mbuild} and {\tt mrun}: \\ \par\medskip
     490      \item<3->[2.]{Restart the shell. Otherwise settings are not active.}\\ \par\medskip
     491      \item<4->[3.]{Create your personal configuration file, needed by {\tt mbuild} and {\tt mrun}: \\ \par\medskip
    566492         \qquad {\tt cd ~/palm/current\_version} \\
    567          \qquad {\tt cp trunk/SCRIPTS/.mrun.config.imuk\_hlrn .mrun.config} \\ \par\medskip
    568          \uncover<6->{
     493         \qquad {\tt cp trunk/SCRIPTS/.mrun.config.cuhk .mrun.config} \\ \par\medskip
     494         \uncover<5->{
    569495         \begin{tikzpicture}[auto, >=latex']
    570496              \hspace{0.5cm}
    … …  
    580506              \path[line] (trunk) -- (scripts);
    581507             
    582               \uncover<7->{\draw [->, thick] {(scripts.south) .. controls (8.0,-1.0) and (4.0,-1.0) .. (currentv.south)};}
     508              \uncover<6->{\draw [->, thick] {(scripts.south) .. controls (8.0,-1.0) and (4.0,-1.0) .. (currentv.south)};}
    583509             
    584510              \node[label, right=0pt of scripts] (scriptlabelbase2) {};
    … …  
    592518\end{frame}
    593519
     520% Folie 14a
     521\begin{frame}
     522   \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Configuring {\tt .mrun.config} on CUHK PCs}
     523   
     524   \tikzstyle{box} = [rectangle, draw, text width=0.9\textwidth, font=\tiny]
     525   
     526   \scriptsize
     527   \begin{itemize}
     528      \item{The only parameter that has to be changed is the hostname.}
     529      \item{You can find out the hostname by running the program ``hostname'' in your terminal.}
     530   \end{itemize}
     531      \begin{center}
     532      \begin{tikzpicture}[auto, node distance=0]     
     533         \node[box](box){
     534            {\tt \# The next line is just an example. Add your own line below or replace this line.} \\
     535            {\tt \%host\_identifier  \textcolor{cyan}{<replace with your hostname>} lccuhk} \\
     536            {\tt \#} \\
     537            {\tt \# The next block contains all informations for compiling the PALM code} \\
     538            {\tt \#} \\
     539            \begin{tabbing}
     540            {\tt \%tmp\_use\_catalog} \hspace{0.3cm} \={\tt /home/student/tmp} \hspace{4.0cm} \={\tt lccuhk parallel} \\
     541            {\tt \%compiler\_name} \>{\tt mpif90} \>{\tt lccuhk parallel} \\
     542            {\tt \%compiler\_name\_ser} \>{\tt ifort} \>{\tt lccuhk parallel} \\
     543            {\tt \%cpp\_options} \>{\tt -D\_\_mpi2:-DMPI\_REAL=MPI\_DOUBLE\_PRECISION:} \>{\tt lccuhk parallel} \\
     544            {\tt } \>{\tt :-DMPI\_2REAL=MPI\_2DOUBLE\_PRECISION:-D\_\_netcdf} \>{\tt } \\
     545            {\tt \%netcdf\_inc} \>{\tt -I:/opt/netcdf-3.6.3/include} \>{\tt lccuhk parallel} \\
     546            {\tt \%netcdf\_lib} \>{\tt -L/opt/netcdf-3.6.3/lib:-lnetcdf} \>{\tt lccuhk parallel} \\
     547            {\tt \%fopts} \>{\tt -xS:-cpp:-openmp:-r8:-nbs:-convert:little\_endian:} \>{\tt lccuhk parallel} \\
     548            {\tt } \>{\tt -I:/opt/mpich2/include} \>{\tt } \\
     549            {\tt \%lopts} \>{\tt -xS:-cpp:-openmp:-r8:-nbs:-Vaxlib:} \>{\tt lccuhk parallel} \\
     550            {\tt } \>{\tt -L/opt/mpich2/lib} \>{\tt } \\
     551            {\tt \%remote\_username} \>{\tt student} \>{\tt lccuhk parallel}
     552            \end{tabbing}};
     553      \end{tikzpicture}
     554      \end{center}
     555\end{frame}
     556
    594557% Folie 16
    595 \begin{frame}
    596    \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Configuration on IMUK-cluster (II)}
    597    
    598    \tikzstyle{box} = [rectangle, draw, text width=0.8\textwidth, font=\tiny]
    599    
    600    \small
    601    \begin{itemize}
    602       \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
    603          \qquad {\tt vi .mrun.config}} \\ \par\medskip
    604       \begin{itemize}
    605       \item<1->{Old: \\
    606    \begin{center}
    607    \begin{tikzpicture}[auto, node distance=0]     
    608       \node[box](box){
    609          .\\.\\
    610          {\tt \# The next block contains all informations for compiling the PALM code}\\ {\tt\#} \\.\\.\\
    611          \begin{tabbing}
    612          {\tt \#\%remote\_username} \hspace{0.2cm}  \={\tt \textcolor{blue}{<replace by your IMUK username>}} \hspace{1.6cm} \={\tt lcmuk parallel} \\
    613          {\tt \#\%tmp\_use\_catalog} \>{\tt /localdata/\textcolor{blue}{<replace by your IMUK username>}} \>{\tt lcmuk parallel}
    614          \end{tabbing}};
    615    \end{tikzpicture}
    616    \end{center}
    617    }
    618    \item<2->{New: \\
    619    \begin{center}
    620    \begin{tikzpicture}[auto, node distance=0]     
    621       \node[box](box){
    622          \begin{tabbing}
    623          {\tt \%remote\_username} \hspace{0.2cm}  \={\tt \textcolor{blue}{your\_name}} \hspace{4.1cm} \={\tt lcmuk parallel} \\
    624          {\tt \%tmp\_use\_catalog} \>{\tt /localdata/\textcolor{blue}{your\_name}} \>{\tt lcmuk parallel}
    625          \end{tabbing}};
    626    \end{tikzpicture}
    627    \end{center}
    628    }
    629       \end{itemize}
    630    \end{itemize}
    631 \end{frame}
     558% \begin{frame}
     559%     \frametitle{Installing PALM on the \textcolor{green}{local} Computer \\ Package Configuration on CUHK PCs (II)}
     560   
     561%    \tikzstyle{box} = [rectangle, draw, text width=0.8\textwidth, font=\tiny]
     562   
     563%    \small
     564%    \begin{itemize}
     565%       \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
     566%          \qquad {\tt vi .mrun.config}} \\ \par\medskip
     567%       \begin{itemize}
     568%       \item<1->{Old: \\
     569%    \begin{center}
     570%    \begin{tikzpicture}[auto, node distance=0]     
     571%       \node[box](box){
     572%          .\\.\\
     573%          {\tt \# The next block contains all informations for compiling the PALM code}\\ {\tt\#} \\.\\.\\
     574%          \begin{tabbing}
     575%          {\tt \#\%remote\_username} \hspace{0.2cm}  \={\tt \textcolor{blue}{<replace by your IMUK username>}} \hspace{1.6cm} \={\tt lcmuk parallel} \\
     576%          {\tt \#\%tmp\_use\_catalog} \>{\tt /localdata/\textcolor{blue}{<replace by your IMUK username>}} \>{\tt lcmuk parallel}
     577%          \end{tabbing}};
     578%    \end{tikzpicture}
     579%    \end{center}
     580%    }
     581%    \item<2->{New: \\
     582%    \begin{center}
     583%    \begin{tikzpicture}[auto, node distance=0]     
     584%       \node[box](box){
     585%          \begin{tabbing}
     586%          {\tt \%remote\_username} \hspace{0.2cm}  \={\tt \textcolor{blue}{your\_name}} \hspace{4.1cm} \={\tt lcmuk parallel} \\
     587%          {\tt \%tmp\_use\_catalog} \>{\tt /localdata/\textcolor{blue}{your\_name}} \>{\tt lcmuk parallel}
     588%          \end{tabbing}};
     589%    \end{tikzpicture}
     590%    \end{center}
     591%    }
     592%       \end{itemize}
     593%    \end{itemize}
     594% \end{frame}
    632595
    633596% Folie 17
    … …  
    800763% Folie 20
    801764\begin{frame}
    802    \frametitle{Checking the PALM Installation (I)}
     765   \frametitle{Checking the PALM Installation (I) \\ on the \textcolor{green}{local} Computer}
    803766   
    804767   \tikzstyle{blanc} = [rectangle, text width=0\textwidth, font=\scriptsize]
    … …  
    866829   Now the job can be run and results can be compared with the reference file
    867830   \begin{itemize}
    868       \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
    869          \qquad {\tt mpd \&} }
    870       \item<3->[2.]{Create and start the (interactive) test run using {\tt mrun}: \\ \par\medskip
     831%       \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
     832%          \qquad {\tt mpd \&} }
     833      \item<2->{Create and start the (interactive) test run using {\tt mrun}: \\ \par\medskip
    871834         \qquad {\tt mrun -d example\_cbl -K parallel -X2 -T2 -r \dq d3\# ts\#\dq} \\ \par\bigskip
    872835      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
    … …  
    878841% Folie 22
    879842\begin{frame}
    880    \frametitle{Checking the PALM Installation (III)}
     843   \frametitle{Checking the PALM Installation (III) \\ on the \textcolor{green}{local} Computer}
    881844   
    882845   \tikzstyle{blanc} = [rectangle, text width=0\textwidth, font=\scriptsize]
    … …  
    932895% Folie 23
    933896\begin{frame}
    934   \frametitle{Installing PALM on IMUK‘s inferno \\ Step by Step Instructions (I)}
     897  \frametitle{Installing PALM on CUHK PCs \\ Step by Step Instructions (I)}
    935898 
    936899  \footnotesize
    937900  \begin{itemize}
    938      \item<2->[1.]{Login on the IMUK-system using the NX-client or an ssh-client:\\ \par\medskip
    939         \qquad {\tt ssh -X \textless your IMUK-username\textgreater @130.75.105.5} \\ \par\medskip
    940      FORTRAN-compiler, MPI- and netCDF-libraries and all other required software are already installed.}
     901     \item<2->[1.]{Log into the CUHK PC using the ``student'' account \\
     902                   and the password ``fed19pa!m''}
     903     FORTRAN-compiler, MPI- and netCDF-libraries and all other required software are already installed.
    941904     \item<3->[2.]{Download the PALM package by using subversion: \\ \par\medskip
    942905        \qquad {\tt mkdir -p $\sim$/palm/current\_version} \\
    943906        \qquad {\tt cd $\sim$/palm/current\_version} \\
    944         \qquad {\tt svn checkout --username \textless your IMUK-username\textgreater \quad \textbackslash} \\
     907        \qquad {\tt svn checkout --username seminar\_cuhk \quad \textbackslash} \\
    945908        \qquad \qquad{\tt svn://130.75.105.7/palm/trunk trunk }}
    946909     \item<4->[3.]{Set environment variables: \\ \par\medskip
    947910        \qquad {\tt export PALM\_BIN=\$HOME/palm/current\_version/trunk/SCRIPTS} \\
    948911        \qquad {\tt export PATH=\$PALM\_BIN:\$PATH} \\ \par\medskip
    949      Set these variables also in file {\tt .myprofile.} or \\ \par\medskip
    950         \qquad {\tt cp /home/raasch/.myprofile \qquad \$HOME}}
     912     Set these variables also in file {\tt .bashrc.}}
    951913  \end{itemize}
    952914\end{frame}
    … …  
    954916% Folie 24
    955917\begin{frame}
    956    \frametitle{Installing PALM on IMUK‘s inferno \\ Step by Step Instructions (II)}
     918   \frametitle{Installing PALM on CUHK PCs \\ Step by Step Instructions (II)}
    957919   
    958920   \footnotesize
    959921   \begin{itemize}
    960922      \item<1->[4.]{A pre-configured configuration file for the IMUK/HLRN system is available: \\ \par\medskip
    961          \qquad{\tt cp trunk/SCRIPTS/.mrun.config.imuk\_hlrn .mrun.config}}\\ \par\medskip
    962       \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!)}
    963       \item<3->[6.]{Create the utility programs: \\ \par\medskip
    964          \qquad {\tt mbuild -u -h lcmuk}}\\ \par\medskip
    965       \item<4->[7.]{Pre-compile the PALM code:\\ \par\medskip
    966          \qquad{\tt mbuild -h lcmuk}}\\ \par\medskip
    967       \item<5->[8.]{Provide the parameter file: \\ \par\medskip
     923         \qquad{\tt cp trunk/SCRIPTS/.mrun.config.cuhk .mrun.config}}\\ \par\medskip
     924      \item<2->[5.]{Create the utility programs: \\ \par\medskip
     925         \qquad {\tt mbuild -u -h lccuhk}}\\ \par\medskip
     926      \item<3->[6.]{Pre-compile the PALM code:\\ \par\medskip
     927         \qquad{\tt mbuild -h lccuhk}}\\ \par\medskip
     928      \item<4->[7.]{Provide the parameter file: \\ \par\medskip
    968929         \qquad{\tt mkdir -p JOBS/example\_cbl/INPUT} \\
    969930         \qquad{\tt cp trunk/INSTALL/example\_cbl\_p3d JOBS/example\_cbl/INPUT}}
    … …  
    973934% Folie 25
    974935\begin{frame}
    975    \frametitle{Installing PALM on IMUK‘s inferno \\ Step by Step Instructions (III)}
     936   \frametitle{Installing PALM on CUHK PCs \\ Step by Step Instructions (III)}
    976937   
    977938   \footnotesize
    978939   \begin{itemize}
    979       \item<1->[9.]{Carry out the test run: \\ \par\medskip
     940      \item<1->[8.]{Carry out the test run: \\ \par\medskip
    980941         \qquad{\tt mrun -d example\_cbl -K parallel -X2 -T2 -r \dq d3\#\dq}}
    981       \item<2->[10.]{Check results (after job has finished): \\ \par\medskip
     942      \item<2->[9.]{Check results (after job has finished): \\ \par\medskip
    982943         \qquad{\tt cd JOBS/example\_cbl/MONITORING} \\
    983944         \qquad{\tt kdiff3 example\_cbl\_rc ../../../trunk/INSTALL/example\_cbl\_rc}}
    … …  
    985946\end{frame}
    986947
    987 % Folie 26
    988 \begin{frame}
    989    \frametitle{Installing PALM on a \textcolor{red}{remote} Computer (HLRN) \\ Step by Step Instructions (I)}
    990    \footnotesize
    991    \begin{itemize}
    992       \item<1->[1.]{Create your working directory on the \textcolor{red}{remote} host: \\ \par\medskip
    993          \qquad {\tt ssh \textless your HLRN-username\textgreater@hicegate.hlrn.de}\\
    994          \qquad {\tt mkdir -p $\sim$/palm/current\_version}} 
    995       \item<2->[2.]{Set environment variables on the \textcolor{red}{remote} host: \\ \par\medskip
    996          \qquad{\tt export PALM\_BIN=\$HOME/palm/current\_version/trunk/SCRIPTS} \\
    997          \qquad{\tt export PATH=\$PALM\_BIN:\$PATH} \\ \par\medskip
    998       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
    999          \qquad{\tt echo \$SHELL}}
    1000       \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.}
    1001    \end{itemize}
    1002 \end{frame}
    1003 
    1004 % Folie 27
    1005 \begin{frame}
    1006    \frametitle{Installing PALM on a \textcolor{red}{remote} Computer (HLRN) \\ Step by Step Instructions (II)}
    1007    \footnotesize
    1008    \begin{itemize}
    1009       \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
    1010       \item<2->[5.]{Create directory {\tt job\_queue} on the \textcolor{green}{local} and the \textcolor{red}{remote} host:\\ \par\medskip
    1011          \qquad{\tt mkdir $\sim$/job\_queue}}
    1012    \end{itemize}
    1013 \end{frame}
    1014 
    1015 % Folie 28
    1016 \begin{frame}
    1017    \frametitle{Establishing the ssh Public-Key Authentication}
    1018    
    1019    \tikzstyle{blue} = [rectangle, draw, align=center, color=green, text width=0.18\textwidth, font=\tiny]
    1020    \tikzstyle{red} = [rectangle, draw, align=center, color=red, text width=0.18\textwidth, font=\tiny]
    1021    \tikzstyle{label} = [rectangle, font=\tiny, minimum size=8pt]
    1022    
    1023    \footnotesize
    1024    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
    1025    Public-key authentication is needed for connections in both directions! \\ \par\medskip
    1026    \begin{center}
    1027       \begin{tikzpicture}[auto, >=latex']
    1028          \coordinate (p0) at (-2.0cm,0.0cm);
    1029          \coordinate (p1) at (2.0cm,0.0cm);
    1030          \coordinate (p2) at (-2.0cm,0.2cm);
    1031          \coordinate (p3) at (2.0cm,0.2cm);
    1032          \coordinate (p4) at (-2.0cm,-0.2cm);
    1033          \coordinate (p5) at (2.0cm,-0.2cm);
    1034          
    1035          \coordinate (p6) at (0.0cm,0.0cm);
    1036          
    1037          \draw[->, thick, color=green] (p2) -- (p3);
    1038          \draw[<-, thick, color=red] (p4) -- (p5);
    1039          
    1040          \node[blue] (green) [left=0.4cm of p0] {
    1041             local computer\\
    1042             \textless{IP-local}\textgreater\\
    1043             OpenSSH
    1044          };
    1045          \node[red] (red) [right=0.4cm of p1] {
    1046             remote computer\\
    1047             \textless{IP-remote}\textgreater\\
    1048             OpenSSH
    1049          };
    1050          
    1051          \node[label, above=0.3cm of p6] (labelblue) {{\tt ssh <HLRN-username>@<130.75.4.101>}};
    1052          \node[label, below=0.3cm of p6] (labelred) {{\tt ssh <HLRN-username>@<130.75.4.101>}};
    1053       \end{tikzpicture}
    1054    \end{center}
    1055    \uncover<2->{Pre-requisites:}\\
    1056    \begin{itemize}
    1057       \item<3->[1.]{On the \textcolor{green}{local} system (IMUK, OpenSSH): create .ssh directory (if not existing):\\ \par\medskip
    1058          \qquad{\tt mkdir $\sim$/.ssh}\\
    1059          \qquad{\tt chmod go-rwx $\sim$/.ssh}} \par\medskip
    1060       \item<4->[2.]{On the \textcolor{red}{remote} system (HLRN, OpenSSH): create .ssh directory (if not existing):\\ \par\medskip
    1061          \qquad{\tt mkdir $\sim$/.ssh}\\
    1062          \qquad{\tt chmod go-rwx $\sim$/.ssh}}
    1063    \end{itemize}
    1064 \end{frame}
    1065 
    1066 % Folie 29
    1067 \begin{frame}
    1068    \frametitle{Enable public-key authentication for connections from the \textcolor{green}{local} system to the \textcolor{red}{remote} system:}
    1069    
    1070    \footnotesize
    1071    On the \textcolor{green}{local} system (inferno.muk.uni-hannover.de, 130.75.105.5):
    1072    \begin{itemize}
    1073       \item<2->[1.]{create the key:\\ \par\medskip
    1074          \qquad{\tt cd $\sim$/.ssh}\\
    1075          \qquad{\tt ssh-keygen -b 2048 -t dsa}\\
    1076          \qquad\qquad{\tt \# creates files id\_dsa and id\_dsa.pub}\\
    1077          \qquad\qquad{\tt \# type <return> when asked for passphrase!!}} \par\medskip
    1078       \item<3->[2.]{copy the public key to the \textcolor{red}{remote} system:\\ \par\medskip
    1079          \qquad{\tt scp id\_dsa.pub <HLRN-usern>@130.75.4.101:.ssh/authorized\_keys}}
    1080    \end{itemize}
    1081 \end{frame}
    1082 
    1083 % Folie 30
    1084 \begin{frame}
    1085    \frametitle{Enable public-key authentication for connections from the \textcolor{red}{remote} system to the \textcolor{green}{local} system:}
    1086    
    1087    \footnotesize
    1088    On the \textcolor{red}{remote} system (hicegate.hlrn.de, 130.75.4.101):
    1089    \begin{itemize}
    1090       \item<2->[1.]{Create the key:\\ \par\medskip
    1091          \qquad{\tt cd $\sim$/.ssh}\\
    1092          \qquad{\tt ssh-keygen -t dsa}\\
    1093          \qquad\qquad{\tt \# creates files id\_dsa and id\_dsa.pub}\\
    1094          \qquad\qquad{\tt \# type <return> when asked for passphrase!!}} \par\medskip
    1095       \item<3->[2.]{Copy the public key to the \textcolor{green}{local} system:\\ \par\medskip
    1096          \qquad{\tt scp id\_dsa.pub <IMUK-usern>@130.75.105.5:.ssh/authorized\_keys}}\\ \par\medskip
    1097       \item<4->[3.]{Append the public key also to the HLRN authorized\_keys file:\\ \par\medskip
    1098          \qquad{\tt cat id\_dsa.pub >> authorized\_keys}}
    1099    \end{itemize}
    1100 \end{frame}
    1101 
    1102 % Folie 31
    1103 \begin{frame}
    1104    \frametitle{Establishing the ssh Public-Key Authentication}
    1105    
    1106    \footnotesize
    1107    \underline{Final action:}\\ \par\medskip
    1108    Establish ssh-connection at least one time from the \textcolor{green}{local} host to the \textcolor{red}{remote} host and vice versa.\\ \par\medskip
    1109    Use IP-adresses (eg. 130.75...) and not the symbolic names (e.g. ...hlrn.de)!\\ \par\medskip
    1110    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
    1111    \begin{itemize}
    1112       \item<2->[1.]{On the \textcolor{green}{local} system (inferno):\\ \par\medskip
    1113          \qquad{\tt ssh <HLRN-username>@130.75.4.101}} \par\medskip
    1114       \item<3->[2.]{On the \textcolor{red}{remote} system (hicegate):\\ \par\medskip
    1115          \qquad{\tt ssh <IMUK-username>@130.75.105.5}}\\
    1116    \end{itemize}
    1117 \end{frame}
    1118 
    1119 % Folie 32
    1120 \begin{frame}
    1121    \frametitle{Installing PALM on a \textcolor{red}{remote} Computer (HLRN) \\ Step by Step Instructions (III)}
    1122    \footnotesize
    1123    \begin{itemize}
    1124       \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
    1125          \qquad{\tt mbuild -u -h lcsgih} \\ \par\medskip
    1126       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
    1127       \item<2->[6.]{Pre-compile the PALM code on the \textcolor{red}{remote} host: \\ \par\medskip
    1128          \qquad{\tt mbuild -h lcsgih}} \\ \par\medskip
    1129       \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
    1130          \qquad{\tt mkdir \textless tmp\_user\_catalog\textgreater}}
    1131    \end{itemize}
    1132 \end{frame}
    1133 
    1134 % Folie 33
    1135 \begin{frame}
    1136    \frametitle{Installing PALM on a \textcolor{red}{remote} Computer (HLRN) \\ Step by Step Instructions (IV)}
    1137    \footnotesize
    1138    \begin{itemize}
    1139       \item<1->[8.]{Carry out the test run by calling mrun on the \textcolor{green}{local} host:\\ \par\medskip
    1140          \qquad{\tt mrun -d example\_cbl -h lcsgih -K parallel -X8 -T2 -q testq}\\
    1141          \qquad{\tt -t 300 -r \dq d3\#\dq}}\\ \par\medskip
    1142       \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
    1143          \qquad{\tt cd JOBS/example\_cbl/MONITORING} \\
    1144          \qquad{\tt kdiff3 lcsgih\_example\_cbl\_rc}\\
    1145          \qquad{\tt ../../../trunk/INSTALL/example\_cbl\_rc}}
    1146    \end{itemize}
    1147 
    1148 \end{frame}
    1149 
    1150 
    1151948\end{document}

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

    r1227 r1234  
    471471   \tikzstyle{greenLarge} = [rectangle, draw, fill=green!20, text width=0.3\textwidth, minimum size=12pt, font=\tiny]
    472472   \tikzstyle{line} = [draw, -]
    473    \tikzstyle{linered} = [draw, color=red, -]
     473
    474474   \tikzstyle{Bigwhite} = [rectangle, text width=0.63\textwidth, minimum size=35pt, font=\tiny]
    475475   \tikzstyle{Bigbox} = [rectangle, draw, fill=gray!20, text width=0.65\textwidth, minimum size=33pt, font=\tiny]
    … …  
    512512%            \uncover<1->{\node [yellowLarge, below=0.05cm of prognosticequca] (prognosticequve) {prognostic\_equations\_vector};}
    513513            \uncover<1->{\node [boxinfo, below=-0.025cm of prognosticequve] (Boxinfo) {For details, see \\ PALM Flow Chart (VIII).};}
    514             \path<1-> [linered] (boxlinespace.north) -| (prognosticequca.north);
     514            \path<1-> [line] (boxlinespace.north) -| (prognosticequca.north);
    515515            \path<1-> [line] (boxlinespace.north) -| (prognosticequve.north);
    516516%            \uncover<1->{\node [redsmall, above=0.3cm of prognosticequca] (redadv) {standard\\advection};}
    … …  
    730730
    731731      \uncover<1->{\node [Bigbox] (bigbox) {};}
    732       \uncover<1->{\node [redsmall, above=-0.23cm of bigbox] (redadv) {standard advection};}
    733 
    734       \uncover<1->{\node [yellow, below=0.1cm of redadv] (calcmeanptprofile) {calc\_mean\_pt\_profile};}
     732
     733      \uncover<1->{\node [yellow, above=-0.75cm of bigbox] (calcmeanptprofile) {calc\_mean\_pt\_profile};}
    735734
    736735%      \uncover<1->{\node [yellowLarge, left=0.5cm of calcmeanptprofile] (prognosticequationsnoopt) {prognostic\_equations\_noopt};}

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

    r1226 r1234  
    306306      \node[green, right=0.6cm of B, text width=14em] (useractions1) {\textcolor{blue}{user\_actions\_(\textit{'before\_timestep'})}};   
    307307         
    308       \node[orange1, below=0.2cm of D] (progeq) {prognostic\_equations};   
    309       \node[orange1, below=0.2cm of E] (progeqfast) {prognostic\_equations\_fast};
    310       \node[draw, fill=red, text width=4em] at (8.6,-0.8) {\textcolor{white}{standard advection}};
    311                
     308      \node[orange1, below=0.2cm of D] (progeq) {prognostic\_equations\_vector};   
     309      \node[orange1, below=0.2cm of E] (progeqfast) {prognostic\_equations\_cache};
     310           
    312311      \node[green, right=0.3cm of progframe, text width=14em] (useractions2) {\textcolor{blue}{user\_actions\_(\textit{'*\_tendency'})}};
    313312     
    … …  
    365364      \draw[-, thick] (B) -- (useractions1);
    366365      \draw[-, thick] (C) -- (D);
     366      \draw[-, thick] (D) -- (E);
     367      \draw[->, thick] (E) -- (progeqfast);
    367368      \draw[-, thick] (progeq) -- (D);     
    368       \draw[-, thick, color=red] (D) -- (E);
    369       \draw[->, thick, color=red] (E) -- (progeqfast);       
    370369      \draw[-, thick] (progframe) -- (useractions2);
    371370      \draw[-, thick] (F) -- (lpm);   
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