--- manual/s_getstarted/text/getting_started.tex	2004/10/14 14:24:28	1.27
+++ manual/s_getstarted/text/getting_started.tex	2015/11/21 03:19:54	1.46
@@ -1,35 +1,25 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.27 2004/10/14 14:24:28 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.46 2015/11/21 03:19:54 dimitri 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}
+\label{sec: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}
+\label{sec: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
@@ -80,7 +63,7 @@
 \end{enumerate}
 
 \subsection{Method 1 - Checkout from CVS}
-\label{sect:cvs_checkout}
+\label{sec: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
@@ -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}
@@ -108,19 +92,23 @@
 
 To obtain the latest sources type:
 \begin{verbatim}
-% cvs co MITgcm
+% cvs co -P MITgcm
 \end{verbatim}
 or to get a specific release type:
 \begin{verbatim}
-% cvs co -P -r checkpoint52i_post  MITgcm
+% cvs co -P -r checkpoint52i_post MITgcm
 \end{verbatim}
+The CVS command ``\texttt{cvs co}'' is the abreviation of the full-name
+``\texttt{cvs checkout}'' command and using the option ``-P'' (\texttt{cvs co -P})
+will prevent to download unnecessary empty directories.
+
 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{rawhtml} <A href="http://mitgcm.org/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
 \begin{verbatim}
-http://mitgcm.org/source_code.html
+http://mitgcm.org/viewvc/MITgcm/MITgcm/
 \end{verbatim}
 \begin{rawhtml} </A> \end{rawhtml}
 
@@ -147,47 +135,32 @@
   \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/public/using_cvs.html" target="idontexist"> \end{rawhtml}
 here
-\begin{rawhtml} </A> \end{rawhtml} 
-.
+\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
+   %  cvs co -P MITgcm_verif_basic
    %  mv MITgcm MITgcm_verif_basic
 \end{verbatim}
 
-
-\subsection{Method 2 - Tar file download}
-\label{sect:conventionalDownload}
-
-If you do not have CVS on your system, you can download the model as a
-tar file from the web site at:
-\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
+Note that it is possible to checkout code without ``cvs login'' and without
+setting any shell environment variables by specifying the pserver name and
+password in one line, for example:
 \begin{verbatim}
-http://mitgcm.org/download/
+   %  cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -P MITgcm
 \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}
 
@@ -199,7 +172,7 @@
 \end{verbatim}
 and then issue the cvs update command such as:
 \begin{verbatim}
-% cvs -q update -r checkpoint52i_post -d -P
+% cvs -q update -d -P -r checkpoint52i_post
 \end{verbatim}
 This will update the ``tag'' to ``checkpoint52i\_post'', add any new
 directories (-d) and remove any empty directories (-P). The -q option
@@ -245,7 +218,7 @@
 latest code'' and we haven't made a ``tag'' or ``release'' since that
 patch then you'll need to get the latest code:
 \begin{verbatim}
-% cvs -q update -A -d -P
+% cvs -q update -d -P -A
 \end{verbatim}
 Unlike, the ``check-out'' and ``update'' procedures above, there is no
 ``tag'' or release name. The -A tells CVS to upgrade to the
@@ -255,7 +228,30 @@
 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{sec: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
@@ -263,307 +259,167 @@
 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 \texttt{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 \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{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}
+\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.
-  
-\item \textit{verification}: this directory contains the model
-  examples. See section \ref{sect:modelExamples}.
-
-\end{itemize}
-
-\section[MITgcm Example Experiments]{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 \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 \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 \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}
+  model output. The subdirectory exch2 contains the code needed for
+  the exch2 package to work with different combinations of domain
+  decompositions.
   
-  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:
+\item \texttt{verification}: this directory contains the model
+  examples. See section \ref{sec:modelExamples}.
 
-  \begin{itemize}
-  \item \textit{input/data}: this file, written as a namelist,
-    specifies the main parameters for the experiment.
+\item \texttt{jobs}: contains sample job scripts for running MITgcm.
   
-  \item \textit{input/data.pkg}: contains parameters relative to the
-    packages used in the experiment.
+\item \texttt{lsopt}: Line search code used for optimization.
   
-  \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}
+\item \texttt{optim}: Interface between MITgcm and line search code.
   
-  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 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
+\label{sec: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{sec: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{sec: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}
 
-In the example above (section \ref{sect:buildingCode}) we built the
+In the example above (section \ref{sec: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
@@ -667,16 +523,30 @@
 
 
 \subsection{Using \texttt{genmake2}}
-\label{sect:genmake}
+\label{sec:genmake}
 
 To compile the code, first use the program \texttt{genmake2} (located
 in the \texttt{tools} directory) to generate a Makefile.
 \texttt{genmake2} is a shell script written to work with all
 ``sh''--compatible shells including bash v1, bash v2, and Bourne.
-Internally, \texttt{genmake2} determines the locations of needed
-files, the compiler, compiler options, libraries, and Unix tools.  It
-relies upon a number of ``optfiles'' located in the
-\texttt{tools/build\_options} directory.
+%Internally, \texttt{genmake2} determines the locations of needed
+%files, the compiler, compiler options, libraries, and Unix tools.  It
+%relies upon a number of ``optfiles'' located in the
+%\texttt{tools/build\_options} directory.
+\texttt{genmake2} parses information from the following sources:
+\begin{description}
+\item[-] a {\em gemake\_local} file if one is found in the current 
+  directory
+\item[-] command-line options
+\item[-] an "options file" as specified by the command-line option
+  \texttt{--optfile=/PATH/FILENAME}
+\item[-] a {\em packages.conf} file (if one is found) with the 
+  specific list of packages to compile. The search path for 
+  file {\em packages.conf} is, first, the current directory and
+  then each of the "MODS" directories in the given order (see below).
+\end{description}
+
+\subsubsection{Optfiles in \texttt{tools/build\_options} directory:}
 
 The purpose of the optfiles is to provide all the compilation options
 for particular ``platforms'' (where ``platform'' roughly means the
@@ -749,6 +619,8 @@
 \begin{rawhtml} </A> \end{rawhtml}
 mailing list.
 
+\subsubsection{Command-line options:}
+
 In addition to the optfiles, \texttt{genmake2} supports a number of
 helpful command-line options.  A complete list of these options can be
 obtained from:
@@ -771,21 +643,31 @@
   the user's path.  When these three items have been identified,
   genmake2 will try to find an optfile that has a matching name.
   
-\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
-  set of packages to be used.  The normal order of precedence for
-  packages is as follows:
-  \begin{enumerate}
-  \item If available, the command line (\texttt{--pdefault}) settings
-    over-rule any others.
-
-  \item Next, \texttt{genmake2} will look for a file named
-    ``\texttt{packages.conf}'' in the local directory or in any of the
-    directories specified with the \texttt{--mods} option.
-    
-  \item Finally, if neither of the above are available,
-    \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
-  \end{enumerate}
+\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
+  directories containing ``modifications''.  These directories contain
+  files with names that may (or may not) exist in the main MITgcm
+  source tree but will be overridden by any identically-named sources
+  within the ``MODS'' directories.
   
+  The order of precedence for this "name-hiding" is as follows:
+  \begin{itemize}
+  \item ``MODS'' directories (in the order given)
+  \item Packages either explicitly specified or provided by default
+    (in the order given)
+  \item Packages included due to package dependencies (in the order
+    that that package dependencies are parsed)
+  \item The "standard dirs" (which may have been specified by the
+    ``-standarddirs'' option)
+  \end{itemize}
+  
+\item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
+  where package groups are defined. If not set, the package-groups 
+  definition will be read from {\em pkg/pkg\_groups}.
+  It also contains the default list of packages (defined
+  as the group ``{\it default\_pkg\_list}'' which is used
+  when no specific package list ({\em packages.conf})
+  is found in current directory or in any "MODS" directory.
+
 \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
   used for packages.
   
@@ -810,26 +692,9 @@
   "STAF" compiler.  As with any compilers, it is helpful to have their
   directories listed in your {\tt \$PATH} environment variable.
   
-\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
-  directories containing ``modifications''.  These directories contain
-  files with names that may (or may not) exist in the main MITgcm
-  source tree but will be overridden by any identically-named sources
-  within the ``MODS'' directories.
-  
-  The order of precedence for this "name-hiding" is as follows:
-  \begin{itemize}
-  \item ``MODS'' directories (in the order given)
-  \item Packages either explicitly specified or provided by default
-    (in the order given)
-  \item Packages included due to package dependencies (in the order
-    that that package dependencies are parsed)
-  \item The "standard dirs" (which may have been specified by the
-    ``-standarddirs'' option)
-  \end{itemize}
-  
 \item[\texttt{--mpi}] This option enables certain MPI features (using
   CPP \texttt{\#define}s) within the code and is necessary for MPI
-  builds (see Section \ref{sect:mpi-build}).
+  builds (see Section \ref{sec:mpi-build}).
   
 \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
   soft-links and other bugs common with the \texttt{make} versions
@@ -852,7 +717,7 @@
 
 
 \subsection{Building with MPI}
-\label{sect:mpi-build}
+\label{sec:mpi-build}
 
 Building MITgcm to use MPI libraries can be complicated due to the
 variety of different MPI implementations available, their dependencies
@@ -867,9 +732,9 @@
   
 \item Determine the locations of your MPI-enabled compiler and/or MPI
   libraries and put them into an options file as described in Section
-  \ref{sect:genmake}.  One can start with one of the examples in:
+  \ref{sec: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/}
@@ -902,7 +767,7 @@
   \end{itemize}
   
 \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
-  (see Section \ref{sect:genmake}) using commands such as:
+  (see Section \ref{sec:genmake}) using commands such as:
 {\footnotesize \begin{verbatim}
   %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
   %  make depend
@@ -920,14 +785,21 @@
   library and a job scheduling and queueing system such as PBS,
   LoadLeveller, Condor, or any of a number of similar tools.  A few
   example scripts (those used for our \begin{rawhtml} <A
-    href="http://mitgcm.org/testing.html"> \end{rawhtml}regular
+    href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
   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/tools/example_scripts/">
+  \end{rawhtml}
+  {\footnotesize \tt
+    http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
+  \begin{rawhtml} </A> \end{rawhtml}
+  or at:
+  \begin{rawhtml} <A
+    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 +820,18 @@
        -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
 \end{verbatim} }
 
-
-
 \section[Running MITgcm]{Running the model in prognostic mode}
-\label{sect:runModel}
+\label{sec:runModel}
+\begin{rawhtml}
+<!-- CMIREDIR:runModel: -->
+\end{rawhtml}
 
-If compilation finished succesfuully (section \ref{sect:buildingCode})
+If compilation finished succesfully (section \ref{sec: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 +841,66 @@
 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 +908,37 @@
 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}
@@ -1059,3 +955,40 @@
 >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
 \end{verbatim}
 
+Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
+they are described in Section \ref{sec:pkg:mnc}.
+
+The MNC output files are all in the ``self-describing'' netCDF
+format and can thus be browsed and/or plotted using tools such as:
+\begin{itemize}
+\item \texttt{ncdump} is a utility which is typically included
+  with every netCDF install:
+  \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
+\begin{verbatim}
+http://www.unidata.ucar.edu/packages/netcdf/
+\end{verbatim}
+  \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
+  binaries into formatted ASCII text files.
+
+\item \texttt{ncview} utility is a very convenient and quick way
+  to plot netCDF data and it runs on most OSes:
+  \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
+\begin{verbatim}
+http://meteora.ucsd.edu/~pierce/ncview_home_page.html
+\end{verbatim}
+  \begin{rawhtml} </A> \end{rawhtml}
+  
+\item MatLAB(c) and other common post-processing environments provide
+  various netCDF interfaces including:
+  \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
+\begin{verbatim}
+http://mexcdf.sourceforge.net/
+\end{verbatim}
+  \begin{rawhtml} </A> \end{rawhtml}
+  \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
+\begin{verbatim}
+http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
+\end{verbatim}
+  \begin{rawhtml} </A> \end{rawhtml}
+\end{itemize}
+