--- manual/s_getstarted/text/getting_started.tex	2001/08/08 16:15:31	1.1
+++ manual/s_getstarted/text/getting_started.tex	2001/12/05 15:49:39	1.12
@@ -1,90 +1,195 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.1 2001/08/08 16:15:31 adcroft Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.12 2001/12/05 15:49:39 adcroft Exp $
 % $Name:  $
 
+%\section{Getting started}
 
-\begin{center}
-{\Large \textbf{Using the model}}
+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
+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.
 
-\vspace*{4mm}
+\section{Where to find information}
+\label{sect:whereToFindInfo}
 
-\vspace*{3mm} {\large July 2001}
-\end{center}
-
-In this part, 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 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 sections 2 and
-3, respectively. In section 4, we provide information on how to customize
-the code when you are ready to try implementing the configuration you have
-in mind.
-
-\section{Getting started}
-
-\subsection{Obtaining the code}
-
-The reference web site for the model is:
+A web site is maintained for release 1 (Sealion) of MITgcm:
 \begin{verbatim}
-http://mitgcm.org
+http://mitgcm.org/sealion
 \end{verbatim}
+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.
 
-On this site, you can download the model as well as find useful information,
-some of which might overlap with what is written here. There is also a
-support news group for the model located at (send your message to \texttt{%
-support@mitgcm.org}):
+There is also a support news group for the model that you can email at
+\texttt{support@mitgcm.org} or browse at:
 \begin{verbatim}
 news://mitgcm.org/mitgcm.support
 \end{verbatim}
+A mail to the email list will reach all the developers and be archived
+on the newsgroup. A users email list will be established at some time
+in the future.
+
+\section{Obtaining the code}
+\label{sect:obtainingCode}
+
+MITgcm can be downloaded from our system by following
+the instructions below. As a courtesy we ask that you send e-mail to us at
+\begin{rawhtml} <A href=mailto:support@mitgcm.org> \end{rawhtml}
+support@mitgcm.org
+\begin{rawhtml} </A> \end{rawhtml}
+to enable us to keep track of who's using the model and in what application.
+You can download the model two ways:
+
+\begin{enumerate}
+\item Using CVS software. CVS is a freely available source code management
+tool. To use CVS you need to have the software installed. Many systems
+come with CVS pre-installed, otherwise good places to look for
+the software for a particular platform are
+\begin{rawhtml} <A href=http://www.cvshome.org/ target="idontexist"> \end{rawhtml}
+cvshome.org
+\begin{rawhtml} </A> \end{rawhtml}
+and
+\begin{rawhtml} <A href=http://www.wincvs.org/ target="idontexist"> \end{rawhtml}
+wincvs.org
+\begin{rawhtml} </A> \end{rawhtml}
+.
+
+\item Using a tar file. This method is simple and does not
+require any special software. However, this method does not
+provide easy support for maintenance updates.
+
+\end{enumerate}
 
 If CVS is available on your system, we strongly encourage you to use it. CVS
 provides an efficient and elegant way of organizing your code and keeping
 track of your changes. If CVS is not available on your machine, you can also
 download a tar file.
 
-\subsubsection{using CVS}
-
 Before you can use CVS, the following environment variable has to be set in
 your .cshrc or .tcshrc:
 \begin{verbatim}
 % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
+\end{verbatim}
+
+To start using CVS, register with the MITgcm CVS server using command:
+\begin{verbatim}
 % cvs login ( CVS password: cvsanon )
 \end{verbatim}
+You only need to do ``cvs login'' once.
 
-You only need to do ``cvs login'' once. To obtain the latest source:
+To obtain the sources for release1 type:
 \begin{verbatim}
-% cvs co -d directory models/MITgcmUV
+% cvs co -d directory -P -r release1_beta1 MITgcm
 \end{verbatim}
 
 This creates a directory called \textit{directory}. If \textit{directory}
 exists this command updates your code based on the repository. Each
 directory in the source tree contains a directory \textit{CVS}. This
 information is required by CVS to keep track of your file versions with
-respect to the repository. Don't edit the files in \textit{CVS}! To obtain a
-specific \textit{version} that is not the latest source:
-\begin{verbatim}
-% cvs co -d directory -r version models/MITgcmUV
-\end{verbatim}
+respect to the repository. Don't edit the files in \textit{CVS}!
+You can also use CVS to download code updates.  More extensive
+information on using CVS for maintaining MITgcm code can be found 
+\begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml}
+here
+\begin{rawhtml} </A> \end{rawhtml} 
+.
 
-\subsubsection{other methods}
 
-You can download the model as a tar file from the reference web site at:
+\paragraph*{Conventional download method}
+\label{sect:conventionalDownload}
+
+If you do not have CVS on your system, you can download the model as a
+tar file from the reference web site at:
+\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
 \begin{verbatim}
 http://mitgcm.org/download/
 \end{verbatim}
-
-\subsection{Model and directory structure}
-
-The ``numerical'' model is contained within a execution environment support
-wrapper. This wrapper is designed to provide a general framework for
-grid-point models. MITgcmUV is a specific numerical model that uses the
-framework. Under this structure the model is split into execution
-environment support code and conventional numerical model code. The
-execution environment support code is held under the \textit{eesupp}
-directory. The grid point model code is held under the \textit{model}
-directory. Code execution actually starts in the \textit{eesupp} routines
-and not in the \textit{model} routines. For this reason the top-level 
+\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.
+
+\paragraph*{Upgrading from an earlier version}
+
+If you already have an earlier version of the code you can ``upgrade''
+your copy instead of downloading the entire repository again. First,
+``cd'' (change directory) to the top of your working copy:
+\begin{verbatim}
+% cd MITgcm
+\end{verbatim}
+and then issue the cvs update command:
+\begin{verbatim}
+% cvs -q update -r release1_beta1 -d -P
+\end{verbatim}
+This will update the ``tag'' to ``release1\_beta1'', add any new
+directories (-d) and remove any empty directories (-P). The -q option
+means be quiet which will reduce the number of messages you'll see in
+the terminal. If you have modified the code prior to upgrading, CVS
+will try to merge your changes with the upgrades. If there is a
+conflict between your modifications and the upgrade, it will report
+that file with a ``C'' in front, e.g.:
+\begin{verbatim}
+C model/src/ini_parms.F
+\end{verbatim}
+If the list of conflicts scrolled off the screen, you can re-issue the
+cvs update command and it will report the conflicts. Conflicts are
+indicated in the code by the delimites ``<<<<<<<'', ``======='' and
+``>>>>>>>''. For example,
+\begin{verbatim}
+<<<<<<< ini_parms.F
+     & bottomDragLinear,myOwnBottomDragCoefficient,
+=======
+     & bottomDragLinear,bottomDragQuadratic,
+>>>>>>> 1.18
+\end{verbatim}
+means that you added ``myOwnBottomDragCoefficient'' to a namelist at
+the same time and place that we added ``bottomDragQuadratic''. You
+need to resolve this conflict and in this case the line should be
+changed to:
+\begin{verbatim}
+     & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
+\end{verbatim}
+and the lines with the delimiters (<<<<<<,======,>>>>>>) be deleted.
+Unless you are making modifications which exactly parallel
+developments we make, these types of conflicts should be rare.
+
+\paragraph*{Upgrading to the current pre-release version}
+
+We don't make a ``release'' for every little patch and bug fix in
+order to keep the frequency of upgrades to a minimum. However, if you
+have run into a problem for which ``we have already fixed in the
+latest code'' and we haven't made a ``tag'' or ``release'' since that
+patch then you'll need to get the latest code:
+\begin{verbatim}
+% cvs -q update -A -d -P
+\end{verbatim}
+Unlike, the ``check-out'' and ``update'' procedures above, there is no
+``tag'' or release name. The -A tells CVS to upgrade to the
+very latest version. As a rule, we don't recommend this since you
+might upgrade while we are in the processes of checking in the code so
+that you may only have part of a patch. Using this method of updating
+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.
+
+\section{Model and directory structure}
+
+The ``numerical'' model is contained within a execution environment
+support wrapper. This wrapper is designed to provide a general
+framework for grid-point models. MITgcmUV is a specific numerical
+model that uses the framework. Under this structure the model is split
+into execution environment support code and conventional numerical
+model code. The execution environment support code is held under the
+\textit{eesupp} directory. The grid point model code is held under the
+\textit{model} directory. Code execution actually starts in the
+\textit{eesupp} routines and not in the \textit{model} routines. For
+this reason the top-level
 \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,
 end-users should not need to worry about this level. The top-level routine
 for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%
@@ -97,7 +202,7 @@
 
 \item \textit{diags}: contains the code relative to time-averaged
 diagnostics. It is subdivided into two subdirectories \textit{inc} and 
-\textit{src} that contain include files (*.\textit{h} files) and fortran
+\textit{src} that contain include files (*.\textit{h} files) and Fortran
 subroutines (*.\textit{F} files), respectively.
 
 \item \textit{doc}: contains brief documentation notes.
@@ -124,53 +229,61 @@
 generates the adjoint code. The latter is described in details in part V.
 
 \item \textit{utils}: this directory contains various utilities. The
-subdirectory \textit{knudsen2} contains code and a makefile that compute
-coefficients of the polynomial approximation to the knudsen formula for an
-ocean nonlinear equation of state. The \textit{matlab} subdirectory contains
-matlab scripts for reading model output directly into matlab. \textit{scripts%
-} contains C-shell post-processing scripts for joining processor-based and
-tiled-based model output.
+subdirectory \textit{knudsen2} contains code and a makefile that
+compute coefficients of the polynomial approximation to the knudsen
+formula for an ocean nonlinear equation of state. The \textit{matlab}
+subdirectory contains matlab scripts for reading model output directly
+into matlab. \textit{scripts} contains C-shell post-processing
+scripts for joining processor-based and tiled-based model output.
 
 \item \textit{verification}: this directory contains the model examples. See
-below.
+section \ref{sect:modelExamples}.
 \end{itemize}
 
-\subsection{Model examples}
+\section{Example experiments}
+\label{sect:modelExamples}
 
-Now that you have successfully downloaded the model code we recommend that
-you first try to run the examples provided with the base version. You will
-probably want to run the example that is the closest to the configuration
-you will use eventually. The examples are located in subdirectories under
-the directory \textit{verification} and are briefly described below (a full
-description is given in section 2):
+The MITgcm distribution comes with a set of twenty-four pre-configured
+numerical experiments. Some of these examples experiments are tests of 
+individual parts of the model code, but many are fully fledged numerical
+simulations. A few of the examples are used for tutorial documentation
+in sections \ref{sect:eg-baro} - \ref{sect:eg-global}. The other examples
+follow the same general structure as the tutorial examples. However,
+they only include brief instructions in a text file called {\it README}.
+The examples are located in subdirectories under
+the directory \textit{verification}. Each
+example is briefly described below.
 
-\subsubsection{List of model examples}
+\subsection{Full list of model examples}
 
-\begin{itemize}
+\begin{enumerate}
 \item \textit{exp0} - single layer, ocean double gyre (barotropic with
-free-surface).
+free-surface). This experiment is described in detail in section
+\ref{sect:eg-baro}.
 
-\item \textit{exp1} - 4 layers, ocean double gyre.
+\item \textit{exp1} - Four layer, ocean double gyre. This experiment is described in detail in section
+\ref{sect:eg-baroc}.
 
 \item \textit{exp2} - 4x4 degree global ocean simulation with steady
-climatological forcing.
+climatological forcing. This experiment is described in detail in section
+\ref{sect:eg-global}.
 
-\item \textit{exp4} - flow over a Gaussian bump in open-water or channel
+\item \textit{exp4} - Flow over a Gaussian bump in open-water or channel
 with open boundaries.
 
-\item \textit{exp5} - inhomogenously forced ocean convection in a doubly
+\item \textit{exp5} - Inhomogenously forced ocean convection in a doubly
 periodic box.
 
-\item \textit{front\_relax} - relaxation of an ocean thermal front (test for
+\item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
 Gent/McWilliams scheme). 2D (Y-Z).
 
-\item \textit{internal wave} - ocean internal wave forced by open boundary
+\item \textit{internal wave} - Ocean internal wave forced by open boundary
 conditions.
 
-\item \textit{natl\_box} - eastern subtropical North Atlantic with KPP
+\item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
 scheme; 1 month integration
 
-\item \textit{hs94.1x64x5} - zonal averaged atmosphere using Held and Suarez
+\item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and Suarez
 '94 forcing.
 
 \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez
@@ -179,26 +292,50 @@
 \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
 Suarez '94 forcing on the cubed sphere.
 
-\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics, 5 layers
-Molteni physics package. Global Zonal Mean configuration, 1x64x5 resolution.
+\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics. Global 
+Zonal Mean configuration, 1x64x5 resolution.
 
 \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric
-physics, 5 layers Molteni physics package. Equatorial Slice configuration.
+physics, equatorial Slice configuration.
 2D (X-Z).
 
 \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
-physics, 5 layers Molteni physics package. 3D Equatorial Channel
-configuration (not completely tested).
+physics. 3D Equatorial Channel configuration.
 
-\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers
-Molteni physics package. Global configuration, 128x64x5 resolution.
+\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
+Global configuration, on latitude longitude grid with 128x64x5 grid points
+($2.8^\circ{\rm degree}$ resolution).
 
-\item \textit{adjustment.128x64x1}
+\item \textit{adjustment.128x64x1} Barotropic adjustment
+problem on latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm degree}$ resolution).
 
 \item \textit{adjustment.cs-32x32x1}
-\end{itemize}
+Barotropic adjustment
+problem on cube sphere grid with 32x32 points per face ( roughly
+$2.8^\circ{\rm degree}$ resolution).
+
+\item \textit{advect\_cs} Two-dimensional passive advection test on
+cube sphere grid.
+
+\item \textit{advect\_xy} Two-dimensional (horizontal plane) passive advection 
+test on Cartesian grid.
+
+\item \textit{advect\_yz} Two-dimensional (vertical plane) passive advection test on Cartesian grid.
+
+\item \textit{carbon} Simple passive tracer experiment. Includes derivative
+calculation. Described in detail in section \ref{sect:eg-carbon-ad}.
 
-\subsubsection{Directory structure of model examples}
+\item \textit{flt\_example} Example of using float package.
+
+\item \textit{global\_ocean.90x40x15} Global circulation with
+GM, flux boundary conditions and poles.
+
+\item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube sphere
+grid.
+
+\end{enumerate}
+
+\subsection{Directory structure of model examples}
 
 Each example directory has the following subdirectories:
 
@@ -223,7 +360,7 @@
 code} depending on the particular experiment. See section 2 for more details.
 
 \item \textit{input}: contains the input data files required to run the
-example. At a mimimum, the \textit{input} directory contains the following
+example. At a minimum, the \textit{input} directory contains the following
 files:
 
 \begin{itemize}
@@ -250,9 +387,165 @@
 Once you have chosen the example you want to run, you are ready to compile
 the code.
 
-\subsection{Compiling the code}
+\section{Building the code}
+\label{sect:buildingCode}
+
+To compile the code, we use the {\em make} program. This uses a file
+({\em Makefile}) that allows us to pre-process source files, specify
+compiler and optimization options and also figures out any file
+dependencies. We supply a script ({\em genmake}), described in section
+\ref{sect:genmake}, that automatically creates the {\em Makefile} for
+you. You then need to build the dependencies and compile the code.
+
+As an example, let's assume that you want to build and run experiment
+\textit{verification/exp2}. The are multiple ways and places to actually
+do this but here let's build the code in
+\textit{verification/exp2/input}:
+\begin{verbatim}
+% cd verification/exp2/input
+\end{verbatim}
+First, build the {\em Makefile}:
+\begin{verbatim}
+% ../../../tools/genmake -mods=../code
+\end{verbatim}
+The command line option tells {\em genmake} to override model source
+code with any files in the directory {\em ./code/}.
+
+If there is no \textit{.genmakerc} in the \textit{input} directory, you have
+to use the following options when invoking \textit{genmake}:
+\begin{verbatim}
+% ../../../tools/genmake  -mods=../code
+\end{verbatim}
+
+Next, create the dependencies:
+\begin{verbatim}
+% make depend
+\end{verbatim}
+This modifies {\em Makefile} by attaching a [long] list of files on
+which other files depend. The purpose of this is to reduce
+re-compilation if and when you start to modify the code. {\tt make
+depend} also created links from the model source to this directory.
+
+Now compile the code:
+\begin{verbatim}
+% make
+\end{verbatim}
+The {\tt make} command creates an executable called \textit{mitgcmuv}.
+
+Now you are ready to run the model. General instructions for doing so are
+given in section \ref{sect:runModel}. Here, we can run the model with:
+\begin{verbatim}
+./mitgcmuv > output.txt
+\end{verbatim}
+where we are re-directing the stream of text output to the file {\em
+output.txt}.
+
+
+\subsection{Building/compiling the code elsewhere}
+
+In the example above (section \ref{sect:buildingCode}) we built the
+executable in the {\em input} directory of the experiment for
+convenience. You can also configure and compile the code in other
+locations, for example on a scratch disk with out having to copy the
+entire source tree. The only requirement to do so is you have {\tt
+genmake} in your path or you know the absolute path to {\tt genmake}.
 
-\subsubsection{The script \textit{genmake}}
+The following sections outline some possible methods of organizing you
+source and data.
+
+\subsubsection{Building from the {\em ../code directory}}
+
+This is just as simple as building in the {\em input/} directory:
+\begin{verbatim}
+% cd verification/exp2/code
+% ../../../tools/genmake
+% make depend
+% make
+\end{verbatim}
+However, to run the model the executable ({\em mitgcmuv}) and input
+files must be in the same place. If you only have one calculation to make:
+\begin{verbatim}
+% cd ../input
+% cp ../code/mitgcmuv ./
+% ./mitgcmuv > output.txt
+\end{verbatim}
+or if you will be making multiple runs with the same executable:
+\begin{verbatim}
+% cd ../
+% cp -r input run1
+% cp code/mitgcmuv run1
+% cd run1
+% ./mitgcmuv > output.txt
+\end{verbatim}
+
+\subsubsection{Building from a new directory}
+
+Since the {\em input} directory contains input files it is often more
+useful to keep {\em input} pristine and build in a new directory
+within {\em verification/exp2/}:
+\begin{verbatim}
+% cd verification/exp2
+% mkdir build
+% cd build
+% ../../../tools/genmake -mods=../code
+% make depend
+% make
+\end{verbatim}
+This builds the code exactly as before but this time you need to copy
+either the executable or the input files or both in order to run the
+model. For example,
+\begin{verbatim}
+% cp ../input/* ./
+% ./mitgcmuv > output.txt
+\end{verbatim}
+or if you tend to make multiple runs with the same executable then
+running in a new directory each time might be more appropriate:
+\begin{verbatim}
+% cd ../
+% mkdir run1
+% cp build/mitgcmuv run1/
+% cp input/* run1/
+% cd run1
+% ./mitgcmuv > output.txt
+\end{verbatim}
+
+\subsubsection{Building from on a scratch disk}
+
+Model object files and output data can use up large amounts of disk
+space so it is often the case that you will be operating on a large
+scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
+following commands will build the model in {\em /scratch/exp2-run1}:
+\begin{verbatim}
+% cd /scratch/exp2-run1
+% ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
+% make depend
+% make
+\end{verbatim}
+To run the model here, you'll need the input files:
+\begin{verbatim}
+% cp ~/MITgcm/verification/exp2/input/* ./
+% ./mitgcmuv > output.txt
+\end{verbatim}
+
+As before, you could build in one directory and make multiple runs of
+the one experiment:
+\begin{verbatim}
+% cd /scratch/exp2
+% mkdir build
+% cd build
+% ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
+% make depend
+% make
+% cd ../
+% cp -r ~/MITgcm/verification/exp2/input run2
+% cd run2
+% ./mitgcmuv > output.txt
+\end{verbatim}
+
+
+
+\subsection{\textit{genmake}}
+\label{sect:genmake}
 
 To compile the code, use the script \textit{genmake} located in the \textit{%
 tools} directory. \textit{genmake} is a script that generates the makefile.
@@ -353,53 +646,37 @@
 that particular example. In this way you don't need to type the options when
 invoking \textit{genmake}.
 
-\subsubsection{Compiling}
 
-Let's assume that you want to run, say, example \textit{exp2} in the \textit{%
-input} directory. To compile the code, type the following commands from the
-model root tree:
-\begin{verbatim}
-% cd verification/exp2/input
-% ../../../tools/genmake
-% make depend
-% make
-\end{verbatim}
+\section{Running the model}
+\label{sect:runModel}
 
-If there is no \textit{.genmakerc} in the \textit{input} directory, you have
-to use the following options when invoking \textit{genmake}:
-\begin{verbatim}
-% ../../../tools/genmake  -mods=../code
-\end{verbatim}
+If compilation finished succesfuully (section \ref{sect:buildModel})
+then an executable called {\em mitgcmuv} will now exist in the local
+directory.
 
-In addition, you will probably want to disable some of the packages. Taking
-again the case of \textit{exp2}, the full \textit{genmake} command will
-probably look like this:
+To run the model as a single process (ie. not in parallel) simply
+type:
 \begin{verbatim}
-% ../../../tools/genmake  -mods=../code  -disable=kpp,gmredi,aim,...
+% ./mitgcmuv
 \end{verbatim}
-
-The make command creates an executable called \textit{mitgcmuv}.
-
-Note that you can compile and run the code in another directory than \textit{%
-input}. You just need to make sure that you copy the input data files into
-the directory where you want to run the model. For example to compile from 
-\textit{code}:
+The ``./'' is a safe-guard to make sure you use the local executable
+in case you have others that exist in your path (surely odd if you
+do!). The above command will spew out many lines of text output to
+your screen.  This output contains details such as parameter values as
+well as diagnostics such as mean Kinetic energy, largest CFL number,
+etc. It is worth keeping this text output with the binary output so we
+normally re-direct the {\em stdout} stream as follows:
 \begin{verbatim}
-% cd verification/exp2/code
-% ../../../tools/genmake
-% make depend
-% make
+% ./mitgcmuv > output.txt
 \end{verbatim}
 
-\subsection{Running the model}
+For the example experiments in {\em vericication}, an example of the
+output is kept in {\em results/output.txt} for comparison. You can compare
+your {\em output.txt} with this one to check that the set-up works.
+
 
-The first thing to do is to run the code by typing \textit{mitgcmuv} and see
-what happens. You can compare what you get with what is in the \textit{%
-results} directory. Unless noted otherwise, most examples are set up to run
-for a few time steps only so that you can quickly figure out whether the
-model is working or not.
 
-\subsubsection{Output files}
+\subsection{Output files}
 
 The model produces various output files. At a minimum, the instantaneous
 ``state'' of the model is written out, which is made of the following files:
@@ -450,7 +727,7 @@
 used to restart the model but are overwritten every other time they are
 output to save disk space during long integrations.
 
-\subsubsection{Looking at the output}
+\subsection{Looking at the output}
 
 All the model data are written according to a ``meta/data'' file format.
 Each variable is associated with two files with suffix names \textit{.data}
@@ -464,11 +741,22 @@
 \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads
 the data. Look at the comments inside the script to see how to use it.
 
-\section{Code structure}
+Some examples of reading and visualizing some output in {\em Matlab}:
+\begin{verbatim}
+% matlab
+>> H=rdmds('Depth');
+>> contourf(H');colorbar;
+>> title('Depth of fluid as used by model');
+
+>> eta=rdmds('Eta',10);
+>> imagesc(eta');axis ij;colorbar;
+>> title('Surface height at iter=10');
 
-\section{Doing it yourself: customizing the code}
+>> eta=rdmds('Eta',[0:10:100]);
+>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
+\end{verbatim}
 
-\subsection{\protect\bigskip Configuration and setup}
+\section{Doing it yourself: customizing the code}
 
 When you are ready to run the model in the configuration you want, the
 easiest thing is to use and adapt the setup of the case studies experiment
@@ -478,6 +766,8 @@
 the ''execution environment'' part is covered in the parallel implementation
 section) and on the variables and parameters that you are likely to change.
 
+\subsection{Configuration and setup}
+
 The CPP keys relative to the ''numerical model'' part of the code are all
 defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{%
 model/inc }or in one of the \textit{code }directories of the case study
@@ -494,7 +784,7 @@
 computational domain, the equations solved in the model, and the simulation
 controls.
 
-\subsubsection{Computational domain, geometry and time-discretization}
+\subsection{Computational domain, geometry and time-discretization}
 
 \begin{itemize}
 \item dimensions
@@ -586,7 +876,7 @@
 stagger baroclinic time stepping can be activated by setting the logical
 variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'.
 
-\subsubsection{Equation of state}
+\subsection{Equation of state}
 
 First, because the model equations are written in terms of perturbations, a
 reference thermodynamic state needs to be specified. This is done through
@@ -615,7 +905,7 @@
 values of the vertical levels in \textit{knudsen2.f }so that they match
 those of your configuration). \textit{\ }
 
-\subsubsection{Momentum equations}
+\subsection{Momentum equations}
 
 In this section, we only focus for now on the parameters that you are likely
 to change, i.e. the ones relative to forcing and dissipation for example.
@@ -719,7 +1009,7 @@
 \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you
 want to deal with the ocean upper or atmosphere lower boundary).
 
-\subsubsection{Tracer equations}
+\subsection{Tracer equations}
 
 This section covers the tracer equations i.e. the potential temperature
 equation and the salinity (for the ocean) or specific humidity (for the
@@ -810,7 +1100,7 @@
 vertically due to static instabilities. Note that \textbf{cadjFreq }and 
 \textbf{ivdc\_kappa }can not both have non-zero value.
 
-\subsubsection{Simulation controls}
+\subsection{Simulation controls}
 
 The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s)
 which determines the IO frequencies and is used in tagging output.
