--- manual/s_getstarted/text/getting_started.tex	2006/06/27 19:08:22	1.36
+++ manual/s_getstarted/text/getting_started.tex	2006/06/30 15:56:52	1.39
@@ -1,19 +1,17 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.36 2006/06/27 19:08:22 molod Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.39 2006/06/30 15:56:52 molod Exp $
 % $Name:  $
 
 %\section{Getting started}
 
-In this section, we describe how to use the model. In the first
-section, we provide enough information to help you get started with
-the model. We believe the best way to familiarize yourself with the
+We believe the best way to familiarize yourself with the
 model is to run the case study examples provided with the base
 version. Information on how to obtain, compile, and run the code is
-found there as well as a brief description of the model structure
-directory and the case study examples.  The latter and the code
-structure are described more fully in chapters
-\ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in
-this section, we provide information on how to customize the code when
-you are ready to try implementing the configuration you have in mind.
+found here as well as a brief description of the model structure
+directory and the case study examples. Information is also provided
+here on how to customize the code when you are ready to try implementing 
+the configuration you have in mind.  The code and algorithm
+are described more fully in chapters \ref{chap:discretization} and 
+\ref{chap:sarch}. 
 
 \section{Where to find information}
 \label{sect:whereToFindInfo}
@@ -21,18 +19,7 @@
 <!-- CMIREDIR:whereToFindInfo: -->
 \end{rawhtml}
 
-A web site is maintained for release 2 (``Pelican'') of MITgcm:
-\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
+There is 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}
@@ -40,16 +27,6 @@
 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}
@@ -175,27 +152,6 @@
    %  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''
@@ -262,6 +218,26 @@
 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: -->
@@ -286,23 +262,12 @@
 
 \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}.
@@ -311,14 +276,17 @@
   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
@@ -327,11 +295,19 @@
   \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}
@@ -916,47 +892,11 @@
 used to restart the model but are overwritten every other time they are
 output to save disk space during long integrations.
 
-
-
 \subsubsection{MNC output files}
 
 Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
 is usually (though not necessarily) placed within a subdirectory with
-a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files
-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}
-
+a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  
 
 \subsection{Looking at the output}
 
@@ -992,3 +932,37 @@
 Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
 they are described in Section \ref{sec:pkg:mnc}.
 
+The MNC output files 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}
+
