/[MITgcm]/manual/s_getstarted/text/getting_started.tex
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revision 1.37 by molod, Wed Jun 28 16:48:19 2006 UTC revision 1.41 by jmc, Fri Jan 22 00:38:16 2010 UTC
# Line 3  Line 3 
3    
4  %\section{Getting started}  %\section{Getting started}
5    
6  In this section, we describe how to use the model. In the first  We believe the best way to familiarize yourself with the
 section, we provide enough information to help you get started with  
 the model. We believe the best way to familiarize yourself with the  
7  model is to run the case study examples provided with the base  model is to run the case study examples provided with the base
8  version. Information on how to obtain, compile, and run the code is  version. Information on how to obtain, compile, and run the code is
9  found there as well as a brief description of the model structure  found here as well as a brief description of the model structure
10  directory and the case study examples.  The latter and the code  directory and the case study examples. Information is also provided
11  structure are described more fully in chapters  here on how to customize the code when you are ready to try implementing
12  \ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in  the configuration you have in mind.  The code and algorithm
13  this section, we provide information on how to customize the code when  are described more fully in chapters \ref{chap:discretization} and
14  you are ready to try implementing the configuration you have in mind.  \ref{chap:sarch}.
15    
16  \section{Where to find information}  \section{Where to find information}
17  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
# Line 104  The MITgcm web site contains further dir Line 102  The MITgcm web site contains further dir
102  code and CVS.  It also contains a web interface to our CVS archive so  code and CVS.  It also contains a web interface to our CVS archive so
103  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
104  development milestones:  development milestones:
105  \begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}  %\begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
106    \begin{rawhtml} <A href="http://mitgcm.org/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
107  \begin{verbatim}  \begin{verbatim}
108  http://mitgcm.org/source_code.html  http://mitgcm.org/source_code.html
109  \end{verbatim}  \end{verbatim}
# Line 141  track of your file versions with respect Line 140  track of your file versions with respect
140  the files in \texttt{CVS}!  You can also use CVS to download code  the files in \texttt{CVS}!  You can also use CVS to download code
141  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
142  MITgcm code can be found  MITgcm code can be found
143  \begin{rawhtml} <A href="http://mitgcm.org/usingcvstoget.html" target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/public/using_cvs.html" target="idontexist"> \end{rawhtml}
144  here  here
145  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
146  .  .
# Line 225  with. So please be sure you understand w Line 224  with. So please be sure you understand w
224    
225  If you do not have CVS on your system, you can download the model as a  If you do not have CVS on your system, you can download the model as a
226  tar file from the web site at:  tar file from the web site at:
227  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/download/ target="idontexist"> \end{rawhtml}
228  \begin{verbatim}  \begin{verbatim}
229  http://mitgcm.org/download/  http://mitgcm.org/download/
230  \end{verbatim}  \end{verbatim}
# Line 717  The steps for building MITgcm with MPI s Line 716  The steps for building MITgcm with MPI s
716    libraries and put them into an options file as described in Section    libraries and put them into an options file as described in Section
717    \ref{sect:genmake}.  One can start with one of the examples in:    \ref{sect:genmake}.  One can start with one of the examples in:
718    \begin{rawhtml} <A    \begin{rawhtml} <A
719      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
720    \end{rawhtml}    \end{rawhtml}
721    \begin{center}    \begin{center}
722      \texttt{MITgcm/tools/build\_options/}      \texttt{MITgcm/tools/build\_options/}
# Line 768  The steps for building MITgcm with MPI s Line 767  The steps for building MITgcm with MPI s
767    library and a job scheduling and queueing system such as PBS,    library and a job scheduling and queueing system such as PBS,
768    LoadLeveller, Condor, or any of a number of similar tools.  A few    LoadLeveller, Condor, or any of a number of similar tools.  A few
769    example scripts (those used for our \begin{rawhtml} <A    example scripts (those used for our \begin{rawhtml} <A
770      href="http://mitgcm.org/testing.html"> \end{rawhtml}regular      href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
771    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
772    at:    at:
773    \begin{rawhtml} <A    \begin{rawhtml} <A
774      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/">
775    \end{rawhtml}    \end{rawhtml}
776    {\footnotesize \tt    {\footnotesize \tt
777      http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }      http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
778      \begin{rawhtml} </A> \end{rawhtml}
779      or at:
780      \begin{rawhtml} <A
781        href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
782      \end{rawhtml}
783      {\footnotesize \tt
784        http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
785    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
786    
787  \end{enumerate}  \end{enumerate}
# Line 894  as the pickup files but are named differ Line 900  as the pickup files but are named differ
900  used to restart the model but are overwritten every other time they are  used to restart the model but are overwritten every other time they are
901  output to save disk space during long integrations.  output to save disk space during long integrations.
902    
   
   
903  \subsubsection{MNC output files}  \subsubsection{MNC output files}
904    
905  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
906  is usually (though not necessarily) placed within a subdirectory with  is usually (though not necessarily) placed within a subdirectory with
907  a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files  a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  
 within this subdirectory are all in the ``self-describing'' netCDF  
 format and can thus be browsed and/or plotted using tools such as:  
 \begin{itemize}  
 \item \texttt{ncdump} is a utility which is typically included  
   with every netCDF install:  
   \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}  
 \begin{verbatim}  
 http://www.unidata.ucar.edu/packages/netcdf/  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF  
   binaries into formatted ASCII text files.  
   
 \item \texttt{ncview} utility is a very convenient and quick way  
   to plot netCDF data and it runs on most OSes:  
   \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}  
 \begin{verbatim}  
 http://meteora.ucsd.edu/~pierce/ncview_home_page.html  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml}  
     
 \item MatLAB(c) and other common post-processing environments provide  
   various netCDF interfaces including:  
   \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}  
 \begin{verbatim}  
 http://mexcdf.sourceforge.net/  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml}  
   \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}  
 \begin{verbatim}  
 http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml}  
 \end{itemize}  
   
908    
909  \subsection{Looking at the output}  \subsection{Looking at the output}
910    
# Line 970  Some examples of reading and visualizing Line 940  Some examples of reading and visualizing
940  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
941  they are described in Section \ref{sec:pkg:mnc}.  they are described in Section \ref{sec:pkg:mnc}.
942    
943    The MNC output files are all in the ``self-describing'' netCDF
944    format and can thus be browsed and/or plotted using tools such as:
945    \begin{itemize}
946    \item \texttt{ncdump} is a utility which is typically included
947      with every netCDF install:
948      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
949    \begin{verbatim}
950    http://www.unidata.ucar.edu/packages/netcdf/
951    \end{verbatim}
952      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
953      binaries into formatted ASCII text files.
954    
955    \item \texttt{ncview} utility is a very convenient and quick way
956      to plot netCDF data and it runs on most OSes:
957      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
958    \begin{verbatim}
959    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
960    \end{verbatim}
961      \begin{rawhtml} </A> \end{rawhtml}
962      
963    \item MatLAB(c) and other common post-processing environments provide
964      various netCDF interfaces including:
965      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
966    \begin{verbatim}
967    http://mexcdf.sourceforge.net/
968    \end{verbatim}
969      \begin{rawhtml} </A> \end{rawhtml}
970      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
971    \begin{verbatim}
972    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
973    \end{verbatim}
974      \begin{rawhtml} </A> \end{rawhtml}
975    \end{itemize}
976    
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