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--- manual/s_getstarted/text/getting_started.tex 2006/06/27 19:08:22 1.36
+++ manual/s_getstarted/text/getting_started.tex 2006/06/28 16:48:19 1.37
@@ -1,4 +1,4 @@
-% $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 1.37 2006/06/28 16:48:19 molod Exp $
% $Name: $
%\section{Getting started}
@@ -21,18 +21,7 @@
<!-- 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 +29,6 @@
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 +154,6 @@
% 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 +220,26 @@
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 +264,12 @@
\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 +278,17 @@
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 +297,19 @@
\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}
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