/[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 1.37 by molod,
Wed Jun 28 16:48:19 2006 UTC
 Line 21 
 you are ready to try implementing the co
  <!-- CMIREDIR:whereToFindInfo: -->
  \end{rawhtml}
- 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
  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
  \begin{verbatim}
-Line 40 
 http://mitgcm.org/mailman/listinfo/mitgc
+Line 29 
 http://mitgcm.org/mailman/listinfo/mitgc
  http://mitgcm.org/pipermail/mitgcm-support/
  \end{verbatim}
  \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
  \section{Obtaining the code}
  \label{sect:obtainingCode}
-Line 175 
 they create can be changed to a differen
+Line 154 
 they create can be changed to a differen
     %  mv MITgcm MITgcm_verif_basic
  \end{verbatim}
- \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.
  \subsubsection{Upgrading from an earlier version}
  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.
  also means we can't tell what version of the code you are working
  with. So please be sure you understand what you're doing.
+ \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.
  \section{Model and directory structure}
  \begin{rawhtml}
  <!-- CMIREDIR:directory_structure: -->
-Line 286 
 structure).
+Line 264 
 structure).
  \begin{itemize}
- \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.
  \item \texttt{doc}: contains brief documentation notes.
  \item \texttt{eesupp}: contains the execution environment source code.
    Also subdivided into two subdirectories \texttt{inc} and
    \texttt{src}.
- \item \texttt{exe}: this directory is initially empty. It is the
-   default directory in which to execute the code.
  \item \texttt{model}: this directory contains the main source code.
    Also subdivided into two subdirectories \texttt{inc} and
    \texttt{src}.
-Line 311 
 structure).
+Line 278 
 structure).
    package corresponds to a subdirectory. For example, \texttt{gmredi}
    contains the code related to the Gent-McWilliams/Redi scheme,
    \texttt{aim} the code relative to the atmospheric intermediate
-   physics. The packages are described in detail in section 3.
+   physics. The packages are described in detail in chapter \ref{chap.packagesI}.
  \item \texttt{tools}: this directory contains various useful tools.
    For example, \texttt{genmake2} is a script written in csh (C-shell)
    that should be used to generate your makefile. The directory
    \texttt{adjoint} contains the makefile specific to the Tangent
    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
-   The latter is described in details in part V.
+   The latter is described in detail in part \ref{chap.ecco}.
+   This directory also contains the subdirectory build\_options, which
+   contains the `optfiles' with the compiler options for the different
+   compilers and machines that can run MITgcm.
  \item \texttt{utils}: this directory contains various utilities. The
    subdirectory \texttt{knudsen2} contains code and a makefile that
-Line 327 
 structure).
+Line 297 
 structure).
    \texttt{matlab} subdirectory contains matlab scripts for reading
    model output directly into matlab. \texttt{scripts} contains C-shell
    post-processing scripts for joining processor-based and tiled-based
-   model output.
+   model output. The subdirectory exch2 contains the code needed for
+   the exch2 package to work with different combinations of domain
+   decompositions.
  \item \texttt{verification}: this directory contains the model
    examples. See section \ref{sect:modelExamples}.
+ \item \texttt{jobs}: contains sample job scripts for running MITgcm.
+ \item \texttt{lsopt}: Line search code used for optimization.
+ \item \texttt{optim}: Interface between MITgcm and line search code.
  \end{itemize}
  \section[Building MITgcm]{Building the code}

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