--- manual/s_getstarted/text/getting_started.tex	2004/06/04 15:32:38	1.25
+++ manual/s_getstarted/text/getting_started.tex	2010/01/21 19:20:08	1.40
@@ -1,35 +1,25 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.25 2004/06/04 15:32:38 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.40 2010/01/21 19:20:08 jmc 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}
+\begin{rawhtml}
+<!-- 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}
@@ -37,19 +27,12 @@
 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}
+\begin{rawhtml}
+<!-- CMIREDIR:obtainingCode: -->
+\end{rawhtml}
 
 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
@@ -79,7 +62,7 @@
 
 \end{enumerate}
 
-\subsubsection{Checkout from CVS}
+\subsection{Method 1 - Checkout from CVS}
 \label{sect:cvs_checkout}
 
 If CVS is available on your system, we strongly encourage you to use it. CVS
@@ -92,7 +75,8 @@
 \begin{verbatim}
 % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
 \end{verbatim}
-in your .cshrc or .tcshrc file.  For bash or sh shells, put:
+in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
+shells, put:
 \begin{verbatim}
 % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
 \end{verbatim}
@@ -118,7 +102,8 @@
 code and CVS.  It also contains a web interface to our CVS archive so
 that one may easily view the state of files, revisions, and other
 development milestones:
-\begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}
+%\begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
+\begin{rawhtml} <A href="http://mitgcm.org/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
 \begin{verbatim}
 http://mitgcm.org/source_code.html
 \end{verbatim}
@@ -147,15 +132,15 @@
   \label{tab:cvsModules}
 \end{table}
 
-The checkout process creates a directory called \textit{MITgcm}. If
-the directory \textit{MITgcm} exists this command updates your code
+The checkout process creates a directory called \texttt{MITgcm}. If
+the directory \texttt{MITgcm} 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
+directory \texttt{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}!  You can also use CVS to download code
+the files in \texttt{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}
+\begin{rawhtml} <A href="http://mitgcm.org/usingcvstoget.html" target="idontexist"> \end{rawhtml}
 here
 \begin{rawhtml} </A> \end{rawhtml} 
 .
@@ -168,27 +153,6 @@
    %  mv MITgcm MITgcm_verif_basic
 \end{verbatim}
 
-
-\subsubsection{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 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''
@@ -255,7 +219,30 @@
 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: -->
+\end{rawhtml}
 
 The ``numerical'' model is contained within a execution environment
 support wrapper. This wrapper is designed to provide a general
@@ -263,303 +250,163 @@
 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
+\texttt{eesupp} directory. The grid point model code is held under the
+\texttt{model} directory. Code execution actually starts in the
+\texttt{eesupp} routines and not in the \texttt{model} routines. For
+this reason the top-level \texttt{MAIN.F} is in the
+\texttt{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}. Here is
+part of the code is in \texttt{model/src/THE\_MODEL\_MAIN.F}. Here is
 a brief description of the directory structure of the model under the
 root tree (a detailed description is given in section 3: Code
 structure).
 
 \begin{itemize}
 
-\item \textit{bin}: this directory is initially empty. It is the
-  default directory in which to compile the code.
-  
-\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 subroutines (*.\textit{F} files), respectively.
-
-\item \textit{doc}: contains brief documentation notes.
-  
-\item \textit{eesupp}: contains the execution environment source code.
-  Also subdivided into two subdirectories \textit{inc} and
-  \textit{src}.
-  
-\item \textit{exe}: this directory is initially empty. It is the
-  default directory in which to execute the code.
+\item \texttt{doc}: contains brief documentation notes.
   
-\item \textit{model}: this directory contains the main source code.
-  Also subdivided into two subdirectories \textit{inc} and
-  \textit{src}.
+\item \texttt{eesupp}: contains the execution environment source code.
+  Also subdivided into two subdirectories \texttt{inc} and
+  \texttt{src}.
+  
+\item \texttt{model}: this directory contains the main source code.
+  Also subdivided into two subdirectories \texttt{inc} and
+  \texttt{src}.
   
-\item \textit{pkg}: contains the source code for the packages. Each
-  package corresponds to a subdirectory. For example, \textit{gmredi}
+\item \texttt{pkg}: contains the source code for the packages. Each
+  package corresponds to a subdirectory. For example, \texttt{gmredi}
   contains the code related to the Gent-McWilliams/Redi scheme,
-  \textit{aim} the code relative to the atmospheric intermediate
-  physics. The packages are described in detail in section 3.
+  \texttt{aim} the code relative to the atmospheric intermediate
+  physics. The packages are described in detail in chapter \ref{chap.packagesI}.
   
-\item \textit{tools}: this directory contains various useful tools.
-  For example, \textit{genmake2} is a script written in csh (C-shell)
+\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
-  \textit{adjoint} contains the makefile specific to the Tangent
+  \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 \textit{utils}: this directory contains various utilities. The
-  subdirectory \textit{knudsen2} contains code and a makefile that
+\item \texttt{utils}: this directory contains various utilities. The
+  subdirectory \texttt{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
+  \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 \textit{verification}: this directory contains the model
+\item \texttt{verification}: this directory contains the model
   examples. See section \ref{sect:modelExamples}.
 
-\end{itemize}
-
-\section{Example experiments}
-\label{sect:modelExamples}
-
-%% a set of twenty-four pre-configured numerical experiments
-
-The MITgcm distribution comes with more than a dozen pre-configured
-numerical experiments. Some of these example 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.
-
-\subsection{Full list of model examples}
-
-\begin{enumerate}
-  
-\item \textit{exp0} - single layer, ocean double gyre (barotropic with
-  free-surface). This experiment is described in detail in section
-  \ref{sect:eg-baro}.
-
-\item \textit{exp1} - Four layer, ocean double gyre. This experiment
-  is described in detail in section \ref{sect:eg-baroc}.
+\item \texttt{jobs}: contains sample job scripts for running MITgcm.
   
-\item \textit{exp2} - 4x4 degree global ocean simulation with steady
-  climatological forcing. This experiment is described in detail in
-  section \ref{sect:eg-global}.
+\item \texttt{lsopt}: Line search code used for optimization.
   
-\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 periodic box.
-
-\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 conditions.
-  
-\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 '94 forcing.
-  
-\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
-  Suarez '94 forcing.
-  
-\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.
-  Global Zonal Mean configuration, 1x64x5 resolution.
-  
-\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
-  Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
-  
-\item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
-  physics. 3D Equatorial Channel configuration.
-  
-\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} Barotropic adjustment problem on
-  latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
-    degree}$ resolution).
-  
-\item \textit{adjustment.cs-32x32x1} 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}.
-
-\item \textit{flt\_example} Example of using float package.
+\item \texttt{optim}: Interface between MITgcm and line search code.
   
-\item \textit{global\_ocean.90x40x15} Global circulation with GM, flux
-  boundary conditions and poles.
-
-\item \textit{global\_ocean\_pressure} Global circulation in pressure
-  coordinate (non-Boussinesq ocean model). Described in detail in
-  section \ref{sect:eg-globalpressure}.
-  
-\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:
-
-\begin{itemize}
-\item \textit{code}: contains the code particular to the example. At a
-  minimum, this directory includes the following files:
-
-  \begin{itemize}
-  \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
-    the ``execution environment'' part of the code. The default
-    version is located in \textit{eesupp/inc}.
-  
-  \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
-    the ``numerical model'' part of the code. The default version is
-    located in \textit{model/inc}.
-  
-  \item \textit{code/SIZE.h}: declares size of underlying
-    computational grid.  The default version is located in
-    \textit{model/inc}.
-  \end{itemize}
-  
-  In addition, other include files and subroutines might be present in
-  \textit{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 minimum, the \textit{input} directory contains the
-  following files:
-
-  \begin{itemize}
-  \item \textit{input/data}: this file, written as a namelist,
-    specifies the main parameters for the experiment.
-  
-  \item \textit{input/data.pkg}: contains parameters relative to the
-    packages used in the experiment.
-  
-  \item \textit{input/eedata}: this file contains ``execution
-    environment'' data. At present, this consists of a specification
-    of the number of threads to use in $X$ and $Y$ under multithreaded
-    execution.
-  \end{itemize}
-  
-  In addition, you will also find in this directory the forcing and
-  topography files as well as the files describing the initial state
-  of the experiment.  This varies from experiment to experiment. See
-  section 2 for more details.
-
-\item \textit{results}: this directory contains the output file
-  \textit{output.txt} produced by the simulation example. This file is
-  useful for comparison with your own output when you run the
-  experiment.
 \end{itemize}
 
-Once you have chosen the example you want to run, you are ready to
-compile the code.
-
-\section{Building the code}
+\section[Building MITgcm]{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 genmake2}), described in
-section \ref{sect:genmake}, that automatically creates the {\em
-  Makefile} for you. You then need to build the dependencies and
+\begin{rawhtml}
+<!-- CMIREDIR:buildingCode: -->
+\end{rawhtml}
+
+To compile the code, we use the \texttt{make} program. This uses a
+file (\texttt{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 (\texttt{genmake2}), described
+in section \ref{sect:genmake}, that automatically creates the
+\texttt{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
+As an example, assume that you want to build and run experiment
+\texttt{verification/exp2}. The are multiple ways and places to
 actually do this but here let's build the code in
-\textit{verification/exp2/input}:
+\texttt{verification/exp2/build}:
 \begin{verbatim}
-% cd verification/exp2/input
+% cd verification/exp2/build
 \end{verbatim}
-First, build the {\em Makefile}:
+First, build the \texttt{Makefile}:
 \begin{verbatim}
 % ../../../tools/genmake2 -mods=../code
 \end{verbatim}
-The command line option tells {\em genmake} to override model source
-code with any files in the directory {\em ./code/}.
+The command line option tells \texttt{genmake} to override model source
+code with any files in the directory \texttt{../code/}.
 
-On many systems, the {\em genmake2} program will be able to
+On many systems, the \texttt{genmake2} program will be able to
 automatically recognize the hardware, find compilers and other tools
-within the user's path (``echo \$PATH''), and then choose an
-appropriate set of options from the files contained in the {\em
-  tools/build\_options} directory.  Under some circumstances, a user
-may have to create a new ``optfile'' in order to specify the exact
-combination of compiler, compiler flags, libraries, and other options
-necessary to build a particular configuration of MITgcm.  In such
-cases, it is generally helpful to read the existing ``optfiles'' and
-mimic their syntax.
+within the user's path (``\texttt{echo \$PATH}''), and then choose an
+appropriate set of options from the files (``optfiles'') contained in
+the \texttt{tools/build\_options} directory.  Under some
+circumstances, a user may have to create a new ``optfile'' in order to
+specify the exact combination of compiler, compiler flags, libraries,
+and other options necessary to build a particular configuration of
+MITgcm.  In such cases, it is generally helpful to read the existing
+``optfiles'' and mimic their syntax.
 
 Through the MITgcm-support list, the MITgcm developers are willing to
 provide help writing or modifing ``optfiles''.  And we encourage users
 to post new ``optfiles'' (particularly ones for new machines or
 architectures) to the 
-\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
+\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
 MITgcm-support@mitgcm.org
 \begin{rawhtml} </A> \end{rawhtml}
 list.
 
-To specify an optfile to {\em genmake2}, the syntax is:
+To specify an optfile to \texttt{genmake2}, the syntax is:
 \begin{verbatim}
 % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
 \end{verbatim}
 
-Once a {\em Makefile} has been generated, we create the dependencies:
+Once a \texttt{Makefile} has been generated, we create the
+dependencies with the command:
 \begin{verbatim}
 % make depend
 \end{verbatim}
-This modifies the {\em Makefile} by attaching a [long] list of files
-upon which other files depend. The purpose of this is to reduce
-re-compilation if and when you start to modify the code. The {\tt make
-  depend} command also creates links from the model source to this
-directory.
+This modifies the \texttt{Makefile} by attaching a (usually, long)
+list of files upon which other files depend. The purpose of this is to
+reduce re-compilation if and when you start to modify the code. The
+{\tt make depend} command also creates links from the model source to
+this directory.  It is important to note that the {\tt make depend}
+stage will occasionally produce warnings or errors since the
+dependency parsing tool is unable to find all of the necessary header
+files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
+is usually OK to ignore the warnings/errors and proceed to the next
+step.
 
-Next compile the code:
+Next one can compile the code using:
 \begin{verbatim}
 % make
 \end{verbatim}
-The {\tt make} command creates an executable called \textit{mitgcmuv}.
+The {\tt make} command creates an executable called \texttt{mitgcmuv}.
 Additional make ``targets'' are defined within the makefile to aid in
-the production of adjoint and other versions of MITgcm.
+the production of adjoint and other versions of MITgcm.  On SMP
+(shared multi-processor) systems, the build process can often be sped
+up appreciably using the command:
+\begin{verbatim}
+% make -j 2
+\end{verbatim}
+where the ``2'' can be replaced with a number that corresponds to the
+number of CPUs available.
 
 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:
+given in section \ref{sect:runModel}. Here, we can run the model by
+first creating links to all the input files:
+\begin{verbatim}
+ln -s ../input/* .
+\end{verbatim}
+and then calling the executable with:
 \begin{verbatim}
 ./mitgcmuv > output.txt
 \end{verbatim}
-where we are re-directing the stream of text output to the file {\em
-output.txt}.
-
+where we are re-directing the stream of text output to the file
+\texttt{output.txt}.
 
 \subsection{Building/compiling the code elsewhere}
 
@@ -869,7 +716,7 @@
   libraries and put them into an options file as described in Section
   \ref{sect:genmake}.  One can start with one of the examples in:
   \begin{rawhtml} <A
-    href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">
+    href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
   \end{rawhtml}
   \begin{center}
     \texttt{MITgcm/tools/build\_options/}
@@ -924,10 +771,10 @@
   verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
   at:
   \begin{rawhtml} <A
-    href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
+    href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
   \end{rawhtml}
   {\footnotesize \tt
-    http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }
+    http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
   \begin{rawhtml} </A> \end{rawhtml}
 
 \end{enumerate}
@@ -948,17 +795,18 @@
        -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
 \end{verbatim} }
 
-
-
-\section{Running the model}
+\section[Running MITgcm]{Running the model in prognostic mode}
 \label{sect:runModel}
+\begin{rawhtml}
+<!-- CMIREDIR:runModel: -->
+\end{rawhtml}
 
-If compilation finished succesfuully (section \ref{sect:buildingCode})
+If compilation finished succesfully (section \ref{sect:buildingCode})
 then an executable called \texttt{mitgcmuv} will now exist in the
 local directory.
 
-To run the model as a single process (ie. not in parallel) simply
-type:
+To run the model as a single process (\textit{ie.} not in parallel)
+simply type:
 \begin{verbatim}
 % ./mitgcmuv
 \end{verbatim}
@@ -968,51 +816,66 @@
 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:
+normally re-direct the \texttt{stdout} stream as follows:
 \begin{verbatim}
 % ./mitgcmuv > output.txt
 \end{verbatim}
-
-For the example experiments in {\em verification}, 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.
+In the event that the model encounters an error and stops, it is very
+helpful to include the last few line of this \texttt{output.txt} file
+along with the (\texttt{stderr}) error message within any bug reports.
+
+For the example experiments in \texttt{verification}, an example of the
+output is kept in \texttt{results/output.txt} for comparison. You can
+compare your \texttt{output.txt} with the corresponding one for that
+experiment to check that the set-up works.
 
 
 
 \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:
+The model produces various output files and, when using \texttt{mnc},
+sometimes even directories.  Depending upon the I/O package(s)
+selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
+both as determined by \texttt{code/packages.conf}) and the run-time
+flags set (in \texttt{input/data.pkg}), the following output may
+appear.
+
+
+\subsubsection{MDSIO output files}
+
+The ``traditional'' output files are generated by the \texttt{mdsio}
+package.  At a minimum, the instantaneous ``state'' of the model is
+written out, which is made of the following files:
 
 \begin{itemize}
-\item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>
-0 $ eastward).
+\item \texttt{U.00000nIter} - zonal component of velocity field (m/s
+  and positive eastward).
 
-\item \textit{V.00000nIter} - meridional component of velocity field (m/s
-and $> 0$ northward).
+\item \texttt{V.00000nIter} - meridional component of velocity field
+  (m/s and positive northward).
 
-\item \textit{W.00000nIter} - vertical component of velocity field (ocean:
-m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure
-i.e. downward).
+\item \texttt{W.00000nIter} - vertical component of velocity field
+  (ocean: m/s and positive upward, atmosphere: Pa/s and positive
+  towards increasing pressure i.e. downward).
 
-\item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,
-atmosphere: $^{0}$K).
+\item \texttt{T.00000nIter} - potential temperature (ocean:
+  $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
 
-\item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor
-(g/kg).
+\item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
+  vapor (g/kg).
 
-\item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:
-surface pressure anomaly (Pa).
+\item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
+  atmosphere: surface pressure anomaly (Pa).
 \end{itemize}
 
-The chain \textit{00000nIter} consists of ten figures that specify the
-iteration number at which the output is written out. For example, \textit{%
-U.0000000300} is the zonal velocity at iteration 300.
+The chain \texttt{00000nIter} consists of ten figures that specify the
+iteration number at which the output is written out. For example,
+\texttt{U.0000000300} is the zonal velocity at iteration 300.
 
 In addition, a ``pickup'' or ``checkpoint'' file called:
 
 \begin{itemize}
-\item \textit{pickup.00000nIter}
+\item \texttt{pickup.00000nIter}
 \end{itemize}
 
 is written out. This file represents the state of the model in a condensed
@@ -1020,29 +883,37 @@
 there is an additional ``pickup'' file:
 
 \begin{itemize}
-\item \textit{pickup\_cd.00000nIter}
+\item \texttt{pickup\_cd.00000nIter}
 \end{itemize}
 
 containing the D-grid velocity data and that has to be written out as well
 in order to restart the integration. Rolling checkpoint files are the same
 as the pickup files but are named differently. Their name contain the chain 
-\textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be
+\texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
 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}}.  
+
 \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}
-and \textit{.meta}. The \textit{.data} file contains the data written in
-binary form (big\_endian by default). The \textit{.meta} file is a
-``header'' file that contains information about the size and the structure
-of the \textit{.data} file. This way of organizing the output is
-particularly useful when running multi-processors calculations. The base
-version of the model includes a few matlab utilities to read output files
-written in this format. The matlab scripts are located in the directory 
-\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.
+The ``traditional'' or mdsio model data are written according to a
+``meta/data'' file format.  Each variable is associated with two files
+with suffix names \texttt{.data} and \texttt{.meta}. The
+\texttt{.data} file contains the data written in binary form
+(big\_endian by default). The \texttt{.meta} file is a ``header'' file
+that contains information about the size and the structure of the
+\texttt{.data} file. This way of organizing the output is particularly
+useful when running multi-processors calculations. The base version of
+the model includes a few matlab utilities to read output files written
+in this format. The matlab scripts are located in the directory
+\texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m}
+reads the data. Look at the comments inside the script to see how to
+use it.
 
 Some examples of reading and visualizing some output in {\em Matlab}:
 \begin{verbatim}
@@ -1059,422 +930,40 @@
 >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
 \end{verbatim}
 
-\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 (described previously) that is the closest to your
-configuration. Then, the amount of setup will be minimized. In this
-section, we focus on the setup relative to the ``numerical model''
-part of the code (the setup relative to 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 experiments under
-\textit{verification.} The model parameters are defined and declared
-in the file \textit{model/inc/PARAMS.h }and their default values are
-set in the routine \textit{model/src/set\_defaults.F. }The default
-values can be modified in the namelist file \textit{data }which needs
-to be located in the directory where you will run the model. The
-parameters are initialized in the routine
-\textit{model/src/ini\_parms.F}.  Look at this routine to see in what
-part of the namelist the parameters are located.
-
-In what follows the parameters are grouped into categories related to
-the computational domain, the equations solved in the model, and the
-simulation controls.
-
-\subsection{Computational domain, geometry and time-discretization}
-
-\begin{description}
-\item[dimensions] \ 
-  
-  The number of points in the x, y, and r directions are represented
-  by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr}
-  respectively which are declared and set in the file
-  \textit{model/inc/SIZE.h}.  (Again, this assumes a mono-processor
-  calculation. For multiprocessor calculations see the section on
-  parallel implementation.)
-
-\item[grid] \ 
-  
-  Three different grids are available: cartesian, spherical polar, and
-  curvilinear (which includes the cubed sphere). The grid is set
-  through the logical variables \textbf{usingCartesianGrid},
-  \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}.
-  In the case of spherical and curvilinear grids, the southern
-  boundary is defined through the variable \textbf{phiMin} which
-  corresponds to the latitude of the southern most cell face (in
-  degrees). The resolution along the x and y directions is controlled
-  by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the
-  case of a cartesian grid, in degrees otherwise).  The vertical grid
-  spacing is set through the 1D array \textbf{delz} for the ocean (in
-  meters) or \textbf{delp} for the atmosphere (in Pa).  The variable
-  \textbf{Ro\_SeaLevel} represents the standard position of Sea-Level
-  in ``R'' coordinate. This is typically set to 0m for the ocean
-  (default value) and 10$^{5}$Pa for the atmosphere. For the
-  atmosphere, also set the logical variable \textbf{groundAtK1} to
-  \texttt{'.TRUE.'} which puts the first level (k=1) at the lower
-  boundary (ground).
-  
-  For the cartesian grid case, the Coriolis parameter $f$ is set
-  through the variables \textbf{f0} and \textbf{beta} which correspond
-  to the reference Coriolis parameter (in s$^{-1}$) and
-  $\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively.
-  If \textbf{beta } is set to a nonzero value, \textbf{f0} is the
-  value of $f$ at the southern edge of the domain.
-
-\item[topography - full and partial cells] \ 
-  
-  The domain bathymetry is read from a file that contains a 2D (x,y)
-  map of depths (in m) for the ocean or pressures (in Pa) for the
-  atmosphere. The file name is represented by the variable
-  \textbf{bathyFile}. The file is assumed to contain binary numbers
-  giving the depth (pressure) of the model at each grid cell, ordered
-  with the x coordinate varying fastest. The points are ordered from
-  low coordinate to high coordinate for both axes. The model code
-  applies without modification to enclosed, periodic, and double
-  periodic domains. Periodicity is assumed by default and is
-  suppressed by setting the depths to 0m for the cells at the limits
-  of the computational domain (note: not sure this is the case for the
-  atmosphere). The precision with which to read the binary data is
-  controlled by the integer variable \textbf{readBinaryPrec} which can
-  take the value \texttt{32} (single precision) or \texttt{64} (double
-  precision). See the matlab program \textit{gendata.m} in the
-  \textit{input} directories under \textit{verification} to see how
-  the bathymetry files are generated for the case study experiments.
-  
-  To use the partial cell capability, the variable \textbf{hFacMin}
-  needs to be set to a value between 0 and 1 (it is set to 1 by
-  default) corresponding to the minimum fractional size of the cell.
-  For example if the bottom cell is 500m thick and \textbf{hFacMin} is
-  set to 0.1, the actual thickness of the cell (i.e. used in the code)
-  can cover a range of discrete values 50m apart from 50m to 500m
-  depending on the value of the bottom depth (in \textbf{bathyFile})
-  at this point.
-  
-  Note that the bottom depths (or pressures) need not coincide with
-  the models levels as deduced from \textbf{delz} or \textbf{delp}.
-  The model will interpolate the numbers in \textbf{bathyFile} so that
-  they match the levels obtained from \textbf{delz} or \textbf{delp}
-  and \textbf{hFacMin}.
-  
-  (Note: the atmospheric case is a bit more complicated than what is
-  written here I think. To come soon...)
-
-\item[time-discretization] \ 
-  
-  The time steps are set through the real variables \textbf{deltaTMom}
-  and \textbf{deltaTtracer} (in s) which represent the time step for
-  the momentum and tracer equations, respectively. For synchronous
-  integrations, simply set the two variables to the same value (or you
-  can prescribe one time step only through the variable
-  \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
-  through the variable \textbf{abEps} (dimensionless). The stagger
-  baroclinic time stepping can be activated by setting the logical
-  variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}.
-
-\end{description}
-
-
-\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 the 1D arrays \textbf{tRef} and \textbf{sRef}.
-\textbf{tRef} specifies the reference potential temperature profile
-(in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting
-from the level k=1. Similarly, \textbf{sRef} specifies the reference
-salinity profile (in ppt) for the ocean or the reference specific
-humidity profile (in g/kg) for the atmosphere.
-
-The form of the equation of state is controlled by the character
-variables \textbf{buoyancyRelation} and \textbf{eosType}.
-\textbf{buoyancyRelation} is set to \texttt{'OCEANIC'} by default and
-needs to be set to \texttt{'ATMOSPHERIC'} for atmosphere simulations.
-In this case, \textbf{eosType} must be set to \texttt{'IDEALGAS'}.
-For the ocean, two forms of the equation of state are available:
-linear (set \textbf{eosType} to \texttt{'LINEAR'}) and a polynomial
-approximation to the full nonlinear equation ( set \textbf{eosType} to
-\texttt{'POLYNOMIAL'}). In the linear case, you need to specify the
-thermal and haline expansion coefficients represented by the variables
-\textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For
-the nonlinear case, you need to generate a file of polynomial
-coefficients called \textit{POLY3.COEFFS}. To do this, use the program
-\textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is
-available in the same directory and you will need to edit the number
-and the values of the vertical levels in \textit{knudsen2.f} so that
-they match those of your configuration).
-
-There there are also higher polynomials for the equation of state:
-\begin{description}
-\item[\texttt{'UNESCO'}:] The UNESCO equation of state formula of
-  Fofonoff and Millard \cite{fofonoff83}. This equation of state
-  assumes in-situ temperature, which is not a model variable; {\em its
-    use is therefore discouraged, and it is only listed for
-    completeness}.
-\item[\texttt{'JMD95Z'}:] A modified UNESCO formula by Jackett and
-  McDougall \cite{jackett95}, which uses the model variable potential
-  temperature as input. The \texttt{'Z'} indicates that this equation
-  of state uses a horizontally and temporally constant pressure
-  $p_{0}=-g\rho_{0}z$. 
-\item[\texttt{'JMD95P'}:] A modified UNESCO formula by Jackett and
-  McDougall \cite{jackett95}, which uses the model variable potential
-  temperature as input. The \texttt{'P'} indicates that this equation
-  of state uses the actual hydrostatic pressure of the last time
-  step. Lagging the pressure in this way requires an additional pickup
-  file for restarts.
-\item[\texttt{'MDJWF'}:] The new, more accurate and less expensive
-  equation of state by McDougall et~al. \cite{mcdougall03}. It also
-  requires lagging the pressure and therefore an additional pickup
-  file for restarts.
-\end{description}
-For none of these options an reference profile of temperature or
-salinity is required.
-
-\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.  The details relevant to the vector-invariant form of the
-equations and the various advection schemes are not covered for the
-moment. We assume that you use the standard form of the momentum
-equations (i.e. the flux-form) with the default advection scheme.
-Also, there are a few logical variables that allow you to turn on/off
-various terms in the momentum equation. These variables are called
-\textbf{momViscosity, momAdvection, momForcing, useCoriolis,
-  momPressureForcing, momStepping} and \textbf{metricTerms }and are
-assumed to be set to \texttt{'.TRUE.'} here.  Look at the file
-\textit{model/inc/PARAMS.h }for a precise definition of these
-variables.
-
-\begin{description}
-\item[initialization] \ 
-  
-  The velocity components are initialized to 0 unless the simulation
-  is starting from a pickup file (see section on simulation control
-  parameters).
-
-\item[forcing] \ 
-  
-  This section only applies to the ocean. You need to generate
-  wind-stress data into two files \textbf{zonalWindFile} and
-  \textbf{meridWindFile} corresponding to the zonal and meridional
-  components of the wind stress, respectively (if you want the stress
-  to be along the direction of only one of the model horizontal axes,
-  you only need to generate one file). The format of the files is
-  similar to the bathymetry file. The zonal (meridional) stress data
-  are assumed to be in Pa and located at U-points (V-points). As for
-  the bathymetry, the precision with which to read the binary data is
-  controlled by the variable \textbf{readBinaryPrec}.  See the matlab
-  program \textit{gendata.m} in the \textit{input} directories under
-  \textit{verification} to see how simple analytical wind forcing data
-  are generated for the case study experiments.
-  
-  There is also the possibility of prescribing time-dependent periodic
-  forcing. To do this, concatenate the successive time records into a
-  single file (for each stress component) ordered in a (x,y,t) fashion
-  and set the following variables: \textbf{periodicExternalForcing }to
-  \texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s)
-  of which the forcing varies (typically 1 month), and
-  \textbf{externForcingCycle} to the repeat time (in s) of the forcing
-  (typically 1 year -- note: \textbf{ externForcingCycle} must be a
-  multiple of \textbf{externForcingPeriod}).  With these variables set
-  up, the model will interpolate the forcing linearly at each
-  iteration.
-
-\item[dissipation] \ 
-  
-  The lateral eddy viscosity coefficient is specified through the
-  variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy
-  viscosity coefficient is specified through the variable
-  \textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and
-  \textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere.  The
-  vertical diffusive fluxes can be computed implicitly by setting the
-  logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}.
-  In addition, biharmonic mixing can be added as well through the
-  variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar
-  grid, you might also need to set the variable \textbf{cosPower}
-  which is set to 0 by default and which represents the power of
-  cosine of latitude to multiply viscosity. Slip or no-slip conditions
-  at lateral and bottom boundaries are specified through the logical
-  variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If
-  set to \texttt{'.FALSE.'}, free-slip boundary conditions are
-  applied. If no-slip boundary conditions are applied at the bottom, a
-  bottom drag can be applied as well. Two forms are available: linear
-  (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and
-  quadratic (set the variable \textbf{bottomDragQuadratic} in
-  m$^{-1}$).
-
-  The Fourier and Shapiro filters are described elsewhere.
-
-\item[C-D scheme] \ 
-  
-  If you run at a sufficiently coarse resolution, you will need the
-  C-D scheme for the computation of the Coriolis terms. The
-  variable\textbf{\ tauCD}, which represents the C-D scheme coupling
-  timescale (in s) needs to be set.
-  
-\item[calculation of pressure/geopotential] \ 
-  
-  First, to run a non-hydrostatic ocean simulation, set the logical
-  variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure
-  field is then inverted through a 3D elliptic equation. (Note: this
-  capability is not available for the atmosphere yet.) By default, a
-  hydrostatic simulation is assumed and a 2D elliptic equation is used
-  to invert the pressure field. The parameters controlling the
-  behaviour of the elliptic solvers are the variables
-  \textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for
-  the 2D case and \textbf{cg3dMaxIters} and
-  \textbf{cg3dTargetResidual} for the 3D case. You probably won't need to
-  alter the default values (are we sure of this?).
-  
-  For the calculation of the surface pressure (for the ocean) or
-  surface geopotential (for the atmosphere) you need to set the
-  logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface}
-  (set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'}
-  depending on how you want to deal with the ocean upper or atmosphere
-  lower boundary).
-
-\end{description} 
-
-\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 atmosphere) equation. As for the momentum equations,
-we only describe for now the parameters that you are likely to change.
-The logical variables \textbf{tempDiffusion} \textbf{tempAdvection}
-\textbf{tempForcing}, and \textbf{tempStepping} allow you to turn
-on/off terms in the temperature equation (same thing for salinity or
-specific humidity with variables \textbf{saltDiffusion},
-\textbf{saltAdvection} etc.). These variables are all assumed here to
-be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h}
-for a precise definition.
-
-\begin{description}
-\item[initialization] \ 
-  
-  The initial tracer data can be contained in the binary files
-  \textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files
-  should contain 3D data ordered in an (x,y,r) fashion with k=1 as the
-  first vertical level.  If no file names are provided, the tracers
-  are then initialized with the values of \textbf{tRef} and
-  \textbf{sRef} mentioned above (in the equation of state section). In
-  this case, the initial tracer data are uniform in x and y for each
-  depth level.
-
-\item[forcing] \ 
-  
-  This part is more relevant for the ocean, the procedure for the
-  atmosphere not being completely stabilized at the moment.
-  
-  A combination of fluxes data and relaxation terms can be used for
-  driving the tracer equations.  For potential temperature, heat flux
-  data (in W/m$ ^{2}$) can be stored in the 2D binary file
-  \textbf{surfQfile}.  Alternatively or in addition, the forcing can
-  be specified through a relaxation term. The SST data to which the
-  model surface temperatures are restored to are supposed to be stored
-  in the 2D binary file \textbf{thetaClimFile}. The corresponding
-  relaxation time scale coefficient is set through the variable
-  \textbf{tauThetaClimRelax} (in s). The same procedure applies for
-  salinity with the variable names \textbf{EmPmRfile},
-  \textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater
-  flux (in m/s) and surface salinity (in ppt) data files and
-  relaxation time scale coefficient (in s), respectively. Also for
-  salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on,
-  natural boundary conditions are applied i.e. when computing the
-  surface salinity tendency, the freshwater flux is multiplied by the
-  model surface salinity instead of a constant salinity value.
-  
-  As for the other input files, the precision with which to read the
-  data is controlled by the variable \textbf{readBinaryPrec}.
-  Time-dependent, periodic forcing can be applied as well following
-  the same procedure used for the wind forcing data (see above).
-
-\item[dissipation] \ 
-  
-  Lateral eddy diffusivities for temperature and salinity/specific
-  humidity are specified through the variables \textbf{diffKhT} and
-  \textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are
-  specified through the variables \textbf{diffKzT} and
-  \textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT
-  }and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The
-  vertical diffusive fluxes can be computed implicitly by setting the
-  logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}.
-  In addition, biharmonic diffusivities can be specified as well
-  through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in
-  m$^{4}$/s). Note that the cosine power scaling (specified through
-  \textbf{cosPower}---see the momentum equations section) is applied to
-  the tracer diffusivities (Laplacian and biharmonic) as well. The
-  Gent and McWilliams parameterization for oceanic tracers is
-  described in the package section. Finally, note that tracers can be
-  also subject to Fourier and Shapiro filtering (see the corresponding
-  section on these filters).
-
-\item[ocean convection] \ 
-  
-  Two options are available to parameterize ocean convection: one is
-  to use the convective adjustment scheme. In this case, you need to
-  set the variable \textbf{cadjFreq}, which represents the frequency
-  (in s) with which the adjustment algorithm is called, to a non-zero
-  value (if set to a negative value by the user, the model will set it
-  to the tracer time step). The other option is to parameterize
-  convection with implicit vertical diffusion. To do this, set the
-  logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}
-  and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s)
-  you wish the tracer vertical diffusivities to have when mixing
-  tracers vertically due to static instabilities. Note that
-  \textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero
-  value.
-
-\end{description}
+Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
+they are described in Section \ref{sec:pkg:mnc}.
 
-\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.  Typically, you will set it to the tracer time step for
-accelerated runs (otherwise it is simply set to the default time step
-\textbf{deltaT}).  Frequency of checkpointing and dumping of the model
-state are referenced to this clock (see below).
+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.
 
-\begin{description}
-\item[run duration] \ 
+\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}
   
-  The beginning of a simulation is set by specifying a start time (in
-  s) through the real variable \textbf{startTime} or by specifying an
-  initial iteration number through the integer variable
-  \textbf{nIter0}. If these variables are set to nonzero values, the
-  model will look for a ''pickup'' file \textit{pickup.0000nIter0} to
-  restart the integration. The end of a simulation is set through the
-  real variable \textbf{endTime} (in s).  Alternatively, you can
-  specify instead the number of time steps to execute through the
-  integer variable \textbf{nTimeSteps}.
-
-\item[frequency of output] \
-  
-  Real variables defining frequencies (in s) with which output files
-  are written on disk need to be set up. \textbf{dumpFreq} controls
-  the frequency with which the instantaneous state of the model is
-  saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output
-  frequency of rolling and permanent checkpoint files, respectively.
-  See section 1.5.1 Output files for the definition of model state and
-  checkpoint files. In addition, time-averaged fields can be written
-  out by setting the variable \textbf{taveFreq} (in s).  The precision
-  with which to write the binary data is controlled by the integer
-  variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or
-  \texttt{64}).
-
-\end{description}
-
+\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}
 
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