--- manual/s_getstarted/text/getting_started.tex	2003/07/30 13:42:52	1.14
+++ manual/s_getstarted/text/getting_started.tex	2006/04/08 15:29:05	1.34
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.14 2003/07/30 13:42:52 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.34 2006/04/08 15:29:05 edhill Exp $
 % $Name:  $
 
 %\section{Getting started}
@@ -15,29 +15,48 @@
 this section, we provide information on how to customize the code when
 you are ready to try implementing the configuration you have in mind.
 
+
 \section{Where to find information}
 \label{sect:whereToFindInfo}
+\begin{rawhtml}
+<!-- CMIREDIR:whereToFindInfo: -->
+\end{rawhtml}
 
-A web site is maintained for release 1 (Sealion) of MITgcm:
+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/sealion
+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.
+documentation, to data-sources, and other related sites.
 
-There is also a support news group for the model that you can email at
-\texttt{MITgcm-support@mitgcm.org} or browse at:
+There is also a web-archived support mailing list for the model that
+you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
+\begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
 \begin{verbatim}
-news://mitgcm.org/mitgcm.support
+http://mitgcm.org/mailman/listinfo/mitgcm-support/
+http://mitgcm.org/pipermail/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.
+\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
@@ -67,46 +86,102 @@
 
 \end{enumerate}
 
+\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
 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.
 
-Before you can use CVS, the following environment variable has to be set in
-your .cshrc or .tcshrc:
+Before you can use CVS, the following environment variable(s) should
+be set within your shell.  For a csh or tcsh shell, put the following 
+\begin{verbatim}
+% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
+\end{verbatim}
+in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
+shells, put:
 \begin{verbatim}
-% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
+% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
 \end{verbatim}
+in your \texttt{.profile} or \texttt{.bashrc} file.
+
 
-To start using CVS, register with the MITgcm CVS server using command:
+To get MITgcm through CVS, first 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 a ``cvs login'' once.
 
-To obtain the sources for release1 type:
+To obtain the latest sources type:
+\begin{verbatim}
+% cvs co MITgcm
+\end{verbatim}
+or to get a specific release type:
+\begin{verbatim}
+% cvs co -P -r checkpoint52i_post  MITgcm
+\end{verbatim}
+The MITgcm web site contains further directions concerning the source
+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{verbatim}
-% cvs co -d directory -P -r release1_beta1 MITgcm
+http://mitgcm.org/source_code.html
 \end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
 
-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}!
-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}
+As a convenience, the MITgcm CVS server contains aliases which are
+named subsets of the codebase.  These aliases can be especially
+helpful when used over slow internet connections or on machines with
+restricted storage space.  Table \ref{tab:cvsModules} contains a list
+of CVS aliases
+\begin{table}[htb]
+  \centering
+  \begin{tabular}[htb]{|lp{3.25in}|}\hline
+    \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline
+    \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\
+    \texttt{MITgcm\_verif\_basic}
+    &  Source code plus a small set of the verification examples 
+    (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5}, 
+    \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\
+    \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\
+    \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\
+    \texttt{MITgcm\_verif\_all}    &  Source code plus all of the
+    verification examples. \\\hline
+  \end{tabular}
+  \caption{MITgcm CVS Modules}
+  \label{tab:cvsModules}
+\end{table}
+
+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 \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 \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}
 here
 \begin{rawhtml} </A> \end{rawhtml} 
 .
+It is important to note that the CVS aliases in Table
+\ref{tab:cvsModules} cannot be used in conjunction with the CVS
+\texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
+they create can be changed to a different name following the check-out:
+\begin{verbatim}
+   %  cvs co MITgcm_verif_basic
+   %  mv MITgcm MITgcm_verif_basic
+\end{verbatim}
 
 
-\paragraph*{Conventional download method}
+\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 reference web site at:
+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/
@@ -114,9 +189,15 @@
 \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.
+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.
 
-\paragraph*{Upgrading from an earlier version}
+\subsubsection{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,
@@ -124,11 +205,11 @@
 \begin{verbatim}
 % cd MITgcm
 \end{verbatim}
-and then issue the cvs update command:
+and then issue the cvs update command such as:
 \begin{verbatim}
-% cvs -q update -r release1_beta1 -d -P
+% cvs -q update -r checkpoint52i_post -d -P
 \end{verbatim}
-This will update the ``tag'' to ``release1\_beta1'', add any new
+This will update the ``tag'' to ``checkpoint52i\_post'', 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
@@ -140,8 +221,9 @@
 \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,
+indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and
+``$>>>>>>>$''. For example,
+{\small
 \begin{verbatim}
 <<<<<<< ini_parms.F
      & bottomDragLinear,myOwnBottomDragCoefficient,
@@ -149,14 +231,17 @@
      & 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:
+{\small
 \begin{verbatim}
      & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
 \end{verbatim}
-and the lines with the delimiters (<<<<<<,======,>>>>>>) be deleted.
+}
+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.
 
@@ -179,6 +264,9 @@
 with. So please be sure you understand what you're doing.
 
 \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
@@ -186,156 +274,169 @@
 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%
-}. 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).
+\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 \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 \textit{model}: this directory contains the main source code. Also
-subdivided into two subdirectories \textit{inc} and \textit{src}.
-
-\item \textit{pkg}: contains the source code for the packages. Each package
-corresponds to a subdirectory. For example, \textit{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.
-
-\item \textit{tools}: this directory contains various useful tools. For
-example, \textit{genmake} 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 linear and Adjoint Compiler (TAMC) that
-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.
+\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}.
+  
+\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,
+  \texttt{aim} the code relative to the atmospheric intermediate
+  physics. The packages are described in detail in section 3.
+  
+\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.
+  
+\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
+  \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.
+  
+\item \texttt{verification}: this directory contains the model
+  examples. See section \ref{sect:modelExamples}.
 
-\item \textit{verification}: this directory contains the model examples. See
-section \ref{sect:modelExamples}.
 \end{itemize}
 
-\section{Example experiments}
+\section[MITgcm Example Experiments]{Example experiments}
 \label{sect:modelExamples}
-
-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.
+\begin{rawhtml}
+<!-- CMIREDIR:modelExamples: -->
+\end{rawhtml}
+
+%% a set of twenty-four pre-configured numerical experiments
+
+The full 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 \texttt{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 \textit{exp2} - 4x4 degree global ocean simulation with steady
-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
-with open boundaries.
-
-\item \textit{exp5} - Inhomogenously forced ocean convection in a doubly
-periodic box.
+  
+\item \texttt{exp0} - single layer, ocean double gyre (barotropic with
+  free-surface). This experiment is described in detail in section
+  \ref{sect:eg-baro}.
+
+\item \texttt{exp1} - Four layer, ocean double gyre. This experiment
+  is described in detail in section \ref{sect:eg-baroc}.
+  
+\item \texttt{exp2} - 4x4 degree global ocean simulation with steady
+  climatological forcing. This experiment is described in detail in
+  section \ref{sect:eg-global}.
+  
+\item \texttt{exp4} - Flow over a Gaussian bump in open-water or
+  channel with open boundaries.
+  
+\item \texttt{exp5} - Inhomogenously forced ocean convection in a
+  doubly periodic box.
 
-\item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
+\item \texttt{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 \texttt{internal wave} - Ocean internal wave forced by open
+  boundary conditions.
+  
+\item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
+  scheme; 1 month integration
+  
+\item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
+  Suarez '94 forcing.
+  
+\item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
+  Suarez '94 forcing.
+  
+\item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
+  Suarez '94 forcing on the cubed sphere.
+  
+\item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
+  Global Zonal Mean configuration, 1x64x5 resolution.
+  
+\item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
+  Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
+  
+\item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
+  physics. 3D Equatorial Channel configuration.
+  
+\item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.
+  Global configuration, on latitude longitude grid with 128x64x5 grid
+  points ($2.8^\circ$ resolution).
+  
+\item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
+  latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
+  
+\item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
+  cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
+  resolution).
+  
+\item \texttt{advect\_cs} Two-dimensional passive advection test on
+  cube sphere grid.
+  
+\item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
+  advection test on Cartesian grid.
+  
+\item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
+  advection test on Cartesian grid.
+  
+\item \texttt{carbon} Simple passive tracer experiment. Includes
+  derivative calculation. Described in detail in section
+  \ref{sect:eg-carbon-ad}.
+
+\item \texttt{flt\_example} Example of using float package.
+  
+\item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
+  boundary conditions and poles.
 
-\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 \textit{global\_ocean.90x40x15} Global circulation with
-GM, flux boundary conditions and poles.
-
-\item \textit{global\_ocean\_pressure} Global circulation in pressure
+\item \texttt{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.
+  
+\item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
+  sphere grid.
 
 \end{enumerate}
 
@@ -344,322 +445,177 @@
 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:
+\item \texttt{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}.
+  \begin{itemize}
+  \item \texttt{code/packages.conf}: declares the list of packages or
+    package groups to be used.  If not included, the default version
+    is located in \texttt{pkg/pkg\_default}.  Package groups are
+    simply convenient collections of commonly used packages which are
+    defined in \texttt{pkg/pkg\_default}.  Some packages may require
+    other packages or may require their absence (that is, they are
+    incompatible) and these package dependencies are listed in
+    \texttt{pkg/pkg\_depend}.
+
+  \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
+    the ``execution environment'' part of the code. The default
+    version is located in \texttt{eesupp/inc}.
+  
+  \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to
+    the ``numerical model'' part of the code. The default version is
+    located in \texttt{model/inc}.
+  
+  \item \texttt{code/SIZE.h}: declares size of underlying
+    computational grid.  The default version is located in
+    \texttt{model/inc}.
+  \end{itemize}
+  
+  In addition, other include files and subroutines might be present in
+  \texttt{code} depending on the particular experiment. See Section 2
+  for more details.
+  
+\item \texttt{input}: contains the input data files required to run
+  the example. At a minimum, the \texttt{input} directory contains the
+  following files:
+
+  \begin{itemize}
+  \item \texttt{input/data}: this file, written as a namelist,
+    specifies the main parameters for the experiment.
+  
+  \item \texttt{input/data.pkg}: contains parameters relative to the
+    packages used in the experiment.
+  
+  \item \texttt{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 \texttt{results}: this directory contains the output file
+  \texttt{output.txt} produced by the simulation example. This file is
+  useful for comparison with your own output when you run the
+  experiment.
 \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:
+Once you have chosen the example you want to run, you are ready to
+compile the code.
 
-\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}
+\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, 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
+\texttt{verification/exp2/build}:
+\begin{verbatim}
+% cd verification/exp2/build
+\end{verbatim}
+First, build the \texttt{Makefile}:
+\begin{verbatim}
+% ../../../tools/genmake2 -mods=../code
+\end{verbatim}
+The command line option tells \texttt{genmake} to override model source
+code with any files in the directory \texttt{../code/}.
+
+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 (``\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}
+MITgcm-support@mitgcm.org
+\begin{rawhtml} </A> \end{rawhtml}
+list.
 
-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}:
+To specify an optfile to \texttt{genmake2}, the syntax is:
 \begin{verbatim}
-% ../../../tools/genmake  -mods=../code
+% ../../../tools/genmake2 -mods=../code -of /path/to/optfile
 \end{verbatim}
 
-Next, 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 {\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.
+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.
 
-Now 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}.
-
-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:
+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.  On SMP
+(shared multi-processor) systems, the build process can often be sped
+up appreciably using the command:
 \begin{verbatim}
-./mitgcmuv > output.txt
+% make -j 2
 \end{verbatim}
-where we are re-directing the stream of text output to the file {\em
-output.txt}.
+where the ``2'' can be replaced with a number that corresponds to the
+number of CPUs available.
 
-
-\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}.
-
-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:
+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 by
+first creating links to all the input files:
 \begin{verbatim}
-% cp ~/MITgcm/verification/exp2/input/* ./
-% ./mitgcmuv > output.txt
+ln -s ../input/* .
 \end{verbatim}
-
-As before, you could build in one directory and make multiple runs of
-the one experiment:
+and then calling the executable with:
 \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
+./mitgcmuv > output.txt
 \end{verbatim}
+where we are re-directing the stream of text output to the file
+\texttt{output.txt}.
 
 
-
-\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.
-It has been written so that the code can be compiled on a wide diversity of
-machines and systems. However, if it doesn't work the first time on your
-platform, you might need to edit certain lines of \textit{genmake} in the
-section containing the setups for the different machines. The file is
-structured like this:
-\begin{verbatim}
-        .
-        .
-        .
-general instructions (machine independent)
-        .
-        .
-        .
-    - setup machine 1
-    - setup machine 2
-    - setup machine 3
-    - setup machine 4
-       etc
-        .
-        .
-        .
-\end{verbatim}
-
-For example, the setup corresponding to a DEC alpha machine is reproduced
-here:
-\begin{verbatim}
-  case OSF1+mpi:
-    echo "Configuring for DEC Alpha"
-    set CPP        = ( '/usr/bin/cpp -P' )
-    set DEFINES    = ( ${DEFINES}  '-DTARGET_DEC -DWORDLENGTH=1' )
-    set KPP        = ( 'kapf' )
-    set KPPFILES   = ( 'main.F' )
-    set KFLAGS1    = ( '-scan=132 -noconc -cmp=' )
-    set FC         = ( 'f77' )
-    set FFLAGS     = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' )
-    set FOPTIM     = ( '-O5 -fast -tune host -inline all' )
-    set NOOPTFLAGS = ( '-O0' )
-    set LIBS       = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' )
-    set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')
-    set RMFILES    = ( '*.p.out' )
-    breaksw
-\end{verbatim}
-
-Typically, these are the lines that you might need to edit to make \textit{%
-genmake} work on your platform if it doesn't work the first time. \textit{%
-genmake} understands several options that are described here:
-
-\begin{itemize}
-\item -rootdir=dir
-
-indicates where the model root directory is relative to the directory where
-you are compiling. This option is not needed if you compile in the \textit{%
-bin} directory (which is the default compilation directory) or within the 
-\textit{verification} tree.
-
-\item -mods=dir1,dir2,...
-
-indicates the relative or absolute paths directories where the sources
-should take precedence over the default versions (located in \textit{model}, 
-\textit{eesupp},...). Typically, this option is used when running the
-examples, see below.
-
-\item -enable=pkg1,pkg2,...
-
-enables packages source code \textit{pkg1}, \textit{pkg2},... when creating
-the makefile.
-
-\item -disable=pkg1,pkg2,...
-
-disables packages source code \textit{pkg1}, \textit{pkg2},... when creating
-the makefile.
-
-\item -platform=machine
-
-specifies the platform for which you want the makefile. In general, you
-won't need this option. \textit{genmake} will select the right machine for
-you (the one you're working on!). However, this option is useful if you have
-a choice of several compilers on one machine and you want to use the one
-that is not the default (ex: \texttt{pgf77} instead of \texttt{f77} under
-Linux).
-
-\item -mpi
-
-this is used when you want to run the model in parallel processing mode
-under mpi (see section on parallel computation for more details).
-
-\item -jam
-
-this is used when you want to run the model in parallel processing mode
-under jam (see section on parallel computation for more details).
-\end{itemize}
-
-For some of the examples, there is a file called \textit{.genmakerc} in the 
-\textit{input} directory that has the relevant \textit{genmake} options for
-that particular example. In this way you don't need to type the options when
-invoking \textit{genmake}.
-
-
-\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 succesfully (section \ref{sect:buildingCode})
+then an executable called \texttt{mitgcmuv} will now exist in the
+local directory.
 
-If compilation finished succesfuully (section \ref{sect:buildModel})
-then an executable called {\em 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}
@@ -669,51 +625,66 @@
 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 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.
+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
@@ -721,29 +692,73 @@
 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}}.  The files
+within this subdirectory are all in the ``self-describing'' netCDF
+format and can thus be browsed and/or plotted using tools such as:
+\begin{itemize}
+\item \texttt{ncdump} is a utility which is typically included
+  with every netCDF install:
+  \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
+\begin{verbatim}
+http://www.unidata.ucar.edu/packages/netcdf/
+\end{verbatim}
+  \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
+  binaries into formatted ASCII text files.
+
+\item \texttt{ncview} utility is a very convenient and quick way
+  to plot netCDF data and it runs on most OSes:
+  \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
+\begin{verbatim}
+http://meteora.ucsd.edu/~pierce/ncview_home_page.html
+\end{verbatim}
+  \begin{rawhtml} </A> \end{rawhtml}
+  
+\item MatLAB(c) and other common post-processing environments provide
+  various netCDF interfaces including:
+  \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
+\begin{verbatim}
+http://mexcdf.sourceforge.net/
+\end{verbatim}
+  \begin{rawhtml} </A> \end{rawhtml}
+  \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
+\begin{verbatim}
+http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
+\end{verbatim}
+  \begin{rawhtml} </A> \end{rawhtml}
+\end{itemize}
+
+
 \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}
@@ -760,415 +775,6 @@
 >> 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{itemize}
-\item dimensions
-\end{itemize}
-
-The number of points in the x, y,\textit{\ }and r\textit{\ }directions are
-represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }%
-and \textbf{Nr}\textit{\ }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 section on parallel
-implementation.)
-
-\begin{itemize}
-\item grid
-\end{itemize}
-
-Three different grids are available: cartesian, spherical polar, and
-curvilinear (including the cubed sphere). The grid is set through the
-logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{%
-usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{%
-usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear
-grids, the southern boundary is defined through the variable \textbf{phiMin}%
-\textit{\ }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}\textit{\ }and \textbf{dely}\textit{\ }(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}\textit{\ }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 put 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}\textit{\ }and \textbf{beta}\textit{\ }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 }\textit{\ }%
-is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
-southern edge of the domain.
-
-\begin{itemize}
-\item topography - full and partial cells
-\end{itemize}
-
-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}\textit{. }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}\textit{\ }%
-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}\textit{\ }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}\textit{\ }or\textit{\ }\textbf{delp}%
-\textit{. }The model will interpolate the numbers in \textbf{bathyFile}%
-\textit{\ }so that they match the levels obtained from \textbf{delz}\textit{%
-\ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
-
-(Note: the atmospheric case is a bit more complicated than what is written
-here I think. To come soon...)
-
-\begin{itemize}
-\item time-discretization
-\end{itemize}
-
-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}.'.
-
-\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}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear
-case, you need to specify the thermal and haline expansion
-coefficients represented by the variables \textbf{tAlpha}\textit{\ 
-  }(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; \emph{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}\textit{, }and \textit{\ }%
-\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{itemize}
-\item initialization
-\end{itemize}
-
-The velocity components are initialized to 0 unless the simulation is
-starting from a pickup file (see section on simulation control parameters).
-
-\begin{itemize}
-\item forcing
-\end{itemize}
-
-This section only applies to the ocean. You need to generate wind-stress
-data into two files \textbf{zonalWindFile}\textit{\ }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}.\textbf{\ }
-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.
-
-\begin{itemize}
-\item dissipation
-\end{itemize}
-
-The lateral eddy viscosity coefficient is specified through the variable 
-\textbf{viscAh}\textit{\ }(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}\textit{\ }(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}\textit{\ }(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}\textit{\ }%
-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}\textit{\ }in s$%
-^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{%
-\ }in m$^{-1}$).
-
-The Fourier and Shapiro filters are described elsewhere.
-
-\begin{itemize}
-\item C-D scheme
-\end{itemize}
-
-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.
-
-\begin{itemize} 
-\item calculation of pressure/geopotential
-\end{itemize} 
-
-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}\textit{\ }and \textbf{cg2dTargetResidual }%
-for the 2D case and \textbf{cg3dMaxIters}\textit{\ }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}\textit{\ }(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).
-
-\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}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{%
-tempForcing}\textit{,} 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}\textit{, }\textbf{%
-saltAdvection}\textit{\ }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{itemize}
-\item initialization
-\end{itemize}
-
-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.
-
-\begin{itemize} 
-\item forcing
-\end{itemize}
-
-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}\textit{. }%
-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}\textit{. }The corresponding relaxation time scale coefficient
-is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The
-same procedure applies for salinity with the variable names \textbf{EmPmRfile%
-}\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}%
-\textit{\ }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).
-
-\begin{itemize}
-\item dissipation
-\end{itemize}
-
-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).
-
-\begin{itemize}
-\item ocean convection
-\end{itemize}
-
-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.
-
-\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).
-
-\begin{itemize}
-\item run duration
-\end{itemize}
-
-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\textit{. }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}. 
-
-\begin{itemize}
-\item frequency of output
-\end{itemize}
+Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
+they are described in Section \ref{sec:pkg:mnc}.
 
-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}).
-
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