/[MITgcm]/manual/s_getstarted/text/getting_started.tex
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revision 1.36 by molod, Tue Jun 27 19:08:22 2006 UTC revision 1.38 by molod, Wed Jun 28 17:20:51 2006 UTC
# Line 21  you are ready to try implementing the co Line 21  you are ready to try implementing the co
21  <!-- CMIREDIR:whereToFindInfo: -->  <!-- CMIREDIR:whereToFindInfo: -->
22  \end{rawhtml}  \end{rawhtml}
23    
24  A web site is maintained for release 2 (``Pelican'') of MITgcm:  There is a web-archived support mailing list for the model that
 \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/pelican  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 Here you will find an on-line version of this document, a  
 ``browsable'' copy of the code and a searchable database of the model  
 and site, as well as links for downloading the model and  
 documentation, to data-sources, and other related sites.  
   
 There is also a web-archived support mailing list for the model that  
25  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
26  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
27  \begin{verbatim}  \begin{verbatim}
# Line 40  http://mitgcm.org/mailman/listinfo/mitgc Line 29  http://mitgcm.org/mailman/listinfo/mitgc
29  http://mitgcm.org/pipermail/mitgcm-support/  http://mitgcm.org/pipermail/mitgcm-support/
30  \end{verbatim}  \end{verbatim}
31  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
 Essentially all of the MITgcm web pages can be searched using a  
 popular web crawler such as Google or through our own search facility:  
 \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/htdig/  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org  
   
   
32    
33  \section{Obtaining the code}  \section{Obtaining the code}
34  \label{sect:obtainingCode}  \label{sect:obtainingCode}
# Line 175  they create can be changed to a differen Line 154  they create can be changed to a differen
154     %  mv MITgcm MITgcm_verif_basic     %  mv MITgcm MITgcm_verif_basic
155  \end{verbatim}  \end{verbatim}
156    
   
 \subsection{Method 2 - Tar file download}  
 \label{sect:conventionalDownload}  
   
 If you do not have CVS on your system, you can download the model as a  
 tar file from the web site at:  
 \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/download/  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 The tar file still contains CVS information which we urge you not to  
 delete; even if you do not use CVS yourself the information can help  
 us if you should need to send us your copy of the code.  If a recent  
 tar file does not exist, then please contact the developers through  
 the  
 \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  
 MITgcm-support@mitgcm.org  
 \begin{rawhtml} </A> \end{rawhtml}  
 mailing list.  
   
157  \subsubsection{Upgrading from an earlier version}  \subsubsection{Upgrading from an earlier version}
158    
159  If you already have an earlier version of the code you can ``upgrade''  If you already have an earlier version of the code you can ``upgrade''
# Line 262  that you may only have part of a patch. Line 220  that you may only have part of a patch.
220  also means we can't tell what version of the code you are working  also means we can't tell what version of the code you are working
221  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
222    
223    \subsection{Method 2 - Tar file download}
224    \label{sect:conventionalDownload}
225    
226    If you do not have CVS on your system, you can download the model as a
227    tar file from the web site at:
228    \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
229    \begin{verbatim}
230    http://mitgcm.org/download/
231    \end{verbatim}
232    \begin{rawhtml} </A> \end{rawhtml}
233    The tar file still contains CVS information which we urge you not to
234    delete; even if you do not use CVS yourself the information can help
235    us if you should need to send us your copy of the code.  If a recent
236    tar file does not exist, then please contact the developers through
237    the
238    \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
239    MITgcm-support@mitgcm.org
240    \begin{rawhtml} </A> \end{rawhtml}
241    mailing list.
242    
243  \section{Model and directory structure}  \section{Model and directory structure}
244  \begin{rawhtml}  \begin{rawhtml}
245  <!-- CMIREDIR:directory_structure: -->  <!-- CMIREDIR:directory_structure: -->
# Line 286  structure). Line 264  structure).
264    
265  \begin{itemize}  \begin{itemize}
266    
 \item \texttt{bin}: this directory is initially empty. It is the  
   default directory in which to compile the code.  
     
 \item \texttt{diags}: contains the code relative to time-averaged  
   diagnostics. It is subdivided into two subdirectories \texttt{inc}  
   and \texttt{src} that contain include files (\texttt{*.h} files) and  
   Fortran subroutines (\texttt{*.F} files), respectively.  
   
267  \item \texttt{doc}: contains brief documentation notes.  \item \texttt{doc}: contains brief documentation notes.
268        
269  \item \texttt{eesupp}: contains the execution environment source code.  \item \texttt{eesupp}: contains the execution environment source code.
270    Also subdivided into two subdirectories \texttt{inc} and    Also subdivided into two subdirectories \texttt{inc} and
271    \texttt{src}.    \texttt{src}.
272        
 \item \texttt{exe}: this directory is initially empty. It is the  
   default directory in which to execute the code.  
     
273  \item \texttt{model}: this directory contains the main source code.  \item \texttt{model}: this directory contains the main source code.
274    Also subdivided into two subdirectories \texttt{inc} and    Also subdivided into two subdirectories \texttt{inc} and
275    \texttt{src}.    \texttt{src}.
# Line 311  structure). Line 278  structure).
278    package corresponds to a subdirectory. For example, \texttt{gmredi}    package corresponds to a subdirectory. For example, \texttt{gmredi}
279    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
280    \texttt{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
281    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in chapter \ref{chap.packagesI}.
282        
283  \item \texttt{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
284    For example, \texttt{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
285    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
286    \texttt{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
287    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
288    The latter is described in details in part V.    The latter is described in detail in part \ref{chap.ecco}.
289      This directory also contains the subdirectory build\_options, which
290      contains the `optfiles' with the compiler options for the different
291      compilers and machines that can run MITgcm.
292        
293  \item \texttt{utils}: this directory contains various utilities. The  \item \texttt{utils}: this directory contains various utilities. The
294    subdirectory \texttt{knudsen2} contains code and a makefile that    subdirectory \texttt{knudsen2} contains code and a makefile that
# Line 327  structure). Line 297  structure).
297    \texttt{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
298    model output directly into matlab. \texttt{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
299    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
300    model output.    model output. The subdirectory exch2 contains the code needed for
301      the exch2 package to work with different combinations of domain
302      decompositions.
303        
304  \item \texttt{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
305    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sect:modelExamples}.
306    
307    \item \texttt{jobs}: contains sample job scripts for running MITgcm.
308      
309    \item \texttt{lsopt}: Line search code used for optimization.
310      
311    \item \texttt{optim}: Interface between MITgcm and line search code.
312      
313  \end{itemize}  \end{itemize}
314    
315  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
# Line 916  as the pickup files but are named differ Line 894  as the pickup files but are named differ
894  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
895  output to save disk space during long integrations.  output to save disk space during long integrations.
896    
   
   
897  \subsubsection{MNC output files}  \subsubsection{MNC output files}
898    
899  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
900  is usually (though not necessarily) placed within a subdirectory with  is usually (though not necessarily) placed within a subdirectory with
901  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}  
   
902    
903  \subsection{Looking at the output}  \subsection{Looking at the output}
904    
# Line 992  Some examples of reading and visualizing Line 934  Some examples of reading and visualizing
934  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
935  they are described in Section \ref{sec:pkg:mnc}.  they are described in Section \ref{sec:pkg:mnc}.
936    
937    The MNC output files are all in the ``self-describing'' netCDF
938    format and can thus be browsed and/or plotted using tools such as:
939    \begin{itemize}
940    \item \texttt{ncdump} is a utility which is typically included
941      with every netCDF install:
942      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
943    \begin{verbatim}
944    http://www.unidata.ucar.edu/packages/netcdf/
945    \end{verbatim}
946      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
947      binaries into formatted ASCII text files.
948    
949    \item \texttt{ncview} utility is a very convenient and quick way
950      to plot netCDF data and it runs on most OSes:
951      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
952    \begin{verbatim}
953    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
954    \end{verbatim}
955      \begin{rawhtml} </A> \end{rawhtml}
956      
957    \item MatLAB(c) and other common post-processing environments provide
958      various netCDF interfaces including:
959      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
960    \begin{verbatim}
961    http://mexcdf.sourceforge.net/
962    \end{verbatim}
963      \begin{rawhtml} </A> \end{rawhtml}
964      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
965    \begin{verbatim}
966    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
967    \end{verbatim}
968      \begin{rawhtml} </A> \end{rawhtml}
969    \end{itemize}
970    
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