--- manual/s_getstarted/text/getting_started.tex	2006/04/05 02:27:33	1.32
+++ manual/s_getstarted/text/getting_started.tex	2010/01/22 00:38:16	1.41
@@ -1,20 +1,17 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.32 2006/04/05 02:27:33 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.41 2010/01/22 00:38:16 jmc Exp $
 % $Name:  $
 
 %\section{Getting started}
 
-In this section, we describe how to use the model. In the first
-section, we provide enough information to help you get started with
-the model. We believe the best way to familiarize yourself with the
+We believe the best way to familiarize yourself with the
 model is to run the case study examples provided with the base
 version. Information on how to obtain, compile, and run the code is
-found there as well as a brief description of the model structure
-directory and the case study examples.  The latter and the code
-structure are described more fully in chapters
-\ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in
-this section, we provide information on how to customize the code when
-you are ready to try implementing the configuration you have in mind.
-
+found here as well as a brief description of the model structure
+directory and the case study examples. Information is also provided
+here on how to customize the code when you are ready to try implementing 
+the configuration you have in mind.  The code and algorithm
+are described more fully in chapters \ref{chap:discretization} and 
+\ref{chap:sarch}. 
 
 \section{Where to find information}
 \label{sect:whereToFindInfo}
@@ -22,18 +19,7 @@
 <!-- CMIREDIR:whereToFindInfo: -->
 \end{rawhtml}
 
-A web site is maintained for release 2 (``Pelican'') of MITgcm:
-\begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
-\begin{verbatim}
-http://mitgcm.org/pelican
-\end{verbatim}
-\begin{rawhtml} </A> \end{rawhtml}
-Here you will find an on-line version of this document, a
-``browsable'' copy of the code and a searchable database of the model
-and site, as well as links for downloading the model and
-documentation, to data-sources, and other related sites.
-
-There is also a web-archived support mailing list for the model that
+There is a web-archived support mailing list for the model that
 you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
 \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
 \begin{verbatim}
@@ -41,16 +27,6 @@
 http://mitgcm.org/pipermail/mitgcm-support/
 \end{verbatim}
 \begin{rawhtml} </A> \end{rawhtml}
-Essentially all of the MITgcm web pages can be searched using a
-popular web crawler such as Google or through our own search facility:
-\begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}
-\begin{verbatim}
-http://mitgcm.org/htdig/
-\end{verbatim}
-\begin{rawhtml} </A> \end{rawhtml}
-%%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
-
-
 
 \section{Obtaining the code}
 \label{sect:obtainingCode}
@@ -126,7 +102,8 @@
 code and CVS.  It also contains a web interface to our CVS archive so
 that one may easily view the state of files, revisions, and other
 development milestones:
-\begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}
+%\begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
+\begin{rawhtml} <A href="http://mitgcm.org/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
 \begin{verbatim}
 http://mitgcm.org/source_code.html
 \end{verbatim}
@@ -163,7 +140,7 @@
 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} 
 .
@@ -176,27 +153,6 @@
    %  mv MITgcm MITgcm_verif_basic
 \end{verbatim}
 
-
-\subsection{Method 2 - Tar file download}
-\label{sect:conventionalDownload}
-
-If you do not have CVS on your system, you can download the model as a
-tar file from the web site at:
-\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
-\begin{verbatim}
-http://mitgcm.org/download/
-\end{verbatim}
-\begin{rawhtml} </A> \end{rawhtml}
-The tar file still contains CVS information which we urge you not to
-delete; even if you do not use CVS yourself the information can help
-us if you should need to send us your copy of the code.  If a recent
-tar file does not exist, then please contact the developers through
-the 
-\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
-MITgcm-support@mitgcm.org
-\begin{rawhtml} </A> \end{rawhtml}
-mailing list.
-
 \subsubsection{Upgrading from an earlier version}
 
 If you already have an earlier version of the code you can ``upgrade''
@@ -263,6 +219,26 @@
 also means we can't tell what version of the code you are working
 with. So please be sure you understand what you're doing.
 
+\subsection{Method 2 - Tar file download}
+\label{sect:conventionalDownload}
+
+If you do not have CVS on your system, you can download the model as a
+tar file from the web site at:
+\begin{rawhtml} <A href=http://mitgcm.org/download/ target="idontexist"> \end{rawhtml}
+\begin{verbatim}
+http://mitgcm.org/download/
+\end{verbatim}
+\begin{rawhtml} </A> \end{rawhtml}
+The tar file still contains CVS information which we urge you not to
+delete; even if you do not use CVS yourself the information can help
+us if you should need to send us your copy of the code.  If a recent
+tar file does not exist, then please contact the developers through
+the 
+\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
+MITgcm-support@mitgcm.org
+\begin{rawhtml} </A> \end{rawhtml}
+mailing list.
+
 \section{Model and directory structure}
 \begin{rawhtml}
 <!-- CMIREDIR:directory_structure: -->
@@ -287,23 +263,12 @@
 
 \begin{itemize}
 
-\item \texttt{bin}: this directory is initially empty. It is the
-  default directory in which to compile the code.
-  
-\item \texttt{diags}: contains the code relative to time-averaged
-  diagnostics. It is subdivided into two subdirectories \texttt{inc}
-  and \texttt{src} that contain include files (\texttt{*.h} files) and
-  Fortran subroutines (\texttt{*.F} files), respectively.
-
 \item \texttt{doc}: contains brief documentation notes.
   
 \item \texttt{eesupp}: contains the execution environment source code.
   Also subdivided into two subdirectories \texttt{inc} and
   \texttt{src}.
   
-\item \texttt{exe}: this directory is initially empty. It is the
-  default directory in which to execute the code.
-  
 \item \texttt{model}: this directory contains the main source code.
   Also subdivided into two subdirectories \texttt{inc} and
   \texttt{src}.
@@ -312,14 +277,17 @@
   package corresponds to a subdirectory. For example, \texttt{gmredi}
   contains the code related to the Gent-McWilliams/Redi scheme,
   \texttt{aim} the code relative to the atmospheric intermediate
-  physics. The packages are described in detail in section 3.
+  physics. The packages are described in detail in chapter \ref{chap.packagesI}.
   
 \item \texttt{tools}: this directory contains various useful tools.
   For example, \texttt{genmake2} is a script written in csh (C-shell)
   that should be used to generate your makefile. The directory
   \texttt{adjoint} contains the makefile specific to the Tangent
   linear and Adjoint Compiler (TAMC) that generates the adjoint code.
-  The latter is described in details in part V.
+  The latter is described in detail in part \ref{chap.ecco}.
+  This directory also contains the subdirectory build\_options, which
+  contains the `optfiles' with the compiler options for the different
+  compilers and machines that can run MITgcm.
   
 \item \texttt{utils}: this directory contains various utilities. The
   subdirectory \texttt{knudsen2} contains code and a makefile that
@@ -328,185 +296,21 @@
   \texttt{matlab} subdirectory contains matlab scripts for reading
   model output directly into matlab. \texttt{scripts} contains C-shell
   post-processing scripts for joining processor-based and tiled-based
-  model output.
+  model output. The subdirectory exch2 contains the code needed for
+  the exch2 package to work with different combinations of domain
+  decompositions.
   
 \item \texttt{verification}: this directory contains the model
   examples. See section \ref{sect:modelExamples}.
 
-\end{itemize}
-
-\section[MITgcm Example Experiments]{Example experiments}
-\label{sect:modelExamples}
-\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 \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 \texttt{front\_relax} - Relaxation of an ocean thermal front (test for
-Gent/McWilliams scheme). 2D (Y-Z).
-
-\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{jobs}: contains sample job scripts for running MITgcm.
   
-\item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
-  Suarez '94 forcing on the cubed sphere.
+\item \texttt{lsopt}: Line search code used for optimization.
   
-\item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
-  Global Zonal Mean configuration, 1x64x5 resolution.
+\item \texttt{optim}: Interface between MITgcm and line search code.
   
-\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 ($2.8^\circ{\rm degree}$ resolution).
-  
-\item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
-  latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
-    degree}$ resolution).
-  
-\item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
-  cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
-    degree}$ 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 \texttt{global\_ocean\_pressure} Global circulation in pressure
-  coordinate (non-Boussinesq ocean model). Described in detail in
-  section \ref{sect:eg-globalpressure}.
-  
-\item \texttt{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 \texttt{code}: contains the code particular to the example. At a
-  minimum, this directory includes the following files:
-
-  \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}
 
-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}
 \begin{rawhtml}
@@ -550,7 +354,7 @@
 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.
@@ -604,6 +408,399 @@
 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
+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
+  genmake2} in your path or you know the absolute path to {\tt
+  genmake2}.
+
+The following sections outline some possible methods of organizing
+your 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/genmake2
+% 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/genmake2 -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 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/genmake2 -rootdir=~/MITgcm \
+  -mods=~/MITgcm/verification/exp2/code
+% make depend
+% make
+\end{verbatim}
+To run the model here, you'll need the input files:
+\begin{verbatim}
+% cp ~/MITgcm/verification/exp2/input/* ./
+% ./mitgcmuv > output.txt
+\end{verbatim}
+
+As before, you could build in one directory and make multiple runs of
+the one experiment:
+\begin{verbatim}
+% cd /scratch/exp2
+% mkdir build
+% cd build
+% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
+  -mods=~/MITgcm/verification/exp2/code
+% make depend
+% make
+% cd ../
+% cp -r ~/MITgcm/verification/exp2/input run2
+% cd run2
+% ./mitgcmuv > output.txt
+\end{verbatim}
+
+
+\subsection{Using \texttt{genmake2}}
+\label{sect: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.
+
+The purpose of the optfiles is to provide all the compilation options
+for particular ``platforms'' (where ``platform'' roughly means the
+combination of the hardware and the compiler) and code configurations.
+Given the combinations of possible compilers and library dependencies
+({\it eg.}  MPI and NetCDF) there may be numerous optfiles available
+for a single machine.  The naming scheme for the majority of the
+optfiles shipped with the code is
+\begin{center}
+  {\bf OS\_HARDWARE\_COMPILER }
+\end{center}
+where
+\begin{description}
+\item[OS] is the name of the operating system (generally the
+  lower-case output of the {\tt 'uname'} command)
+\item[HARDWARE] is a string that describes the CPU type and
+  corresponds to output from the  {\tt 'uname -m'} command:
+  \begin{description}
+  \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
+    and athlon
+  \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
+  \item[amd64] is AMD x86\_64 systems
+  \item[ppc] is for Mac PowerPC systems
+  \end{description}
+\item[COMPILER] is the compiler name (generally, the name of the
+  FORTRAN executable)
+\end{description}
+
+In many cases, the default optfiles are sufficient and will result in
+usable Makefiles.  However, for some machines or code configurations,
+new ``optfiles'' must be written. To create a new optfile, it is
+generally best to start with one of the defaults and modify it to suit
+your needs.  Like \texttt{genmake2}, the optfiles are all written
+using a simple ``sh''--compatible syntax.  While nearly all variables
+used within \texttt{genmake2} may be specified in the optfiles, the
+critical ones that should be defined are:
+
+\begin{description}
+\item[FC] the FORTRAN compiler (executable) to use
+\item[DEFINES] the command-line DEFINE options passed to the compiler
+\item[CPP] the C pre-processor to use
+\item[NOOPTFLAGS] options flags for special files that should not be
+  optimized
+\end{description}
+
+For example, the optfile for a typical Red Hat Linux machine (``ia32''
+architecture) using the GCC (g77) compiler is
+\begin{verbatim}
+FC=g77
+DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
+CPP='cpp  -traditional -P'
+NOOPTFLAGS='-O0'
+#  For IEEE, use the "-ffloat-store" option
+if test "x$IEEE" = x ; then
+    FFLAGS='-Wimplicit -Wunused -Wuninitialized'
+    FOPTIM='-O3 -malign-double -funroll-loops'
+else
+    FFLAGS='-Wimplicit -Wunused -ffloat-store'
+    FOPTIM='-O0 -malign-double'
+fi
+\end{verbatim}
+
+If you write an optfile for an unrepresented machine or compiler, you
+are strongly encouraged to submit the optfile to the MITgcm project
+for inclusion.  Please send the file to the
+\begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
+\begin{center}
+  MITgcm-support@mitgcm.org
+\end{center}
+\begin{rawhtml} </A> \end{rawhtml}
+mailing list.
+
+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:
+\begin{verbatim}
+% genmake2 -h
+\end{verbatim}
+
+The most important command-line options are:
+\begin{description}
+  
+\item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
+  should be used for a particular build.
+  
+  If no "optfile" is specified (either through the command line or the
+  MITGCM\_OPTFILE environment variable), genmake2 will try to make a
+  reasonable guess from the list provided in {\em
+    tools/build\_options}.  The method used for making this guess is
+  to first determine the combination of operating system and hardware
+  (eg. "linux\_ia32") and then find a working FORTRAN compiler within
+  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{--pdepend=/PATH/FILENAME}] specifies the dependency file
+  used for packages.
+  
+  If not specified, the default dependency file {\em pkg/pkg\_depend}
+  is used.  The syntax for this file is parsed on a line-by-line basis
+  where each line containes either a comment ("\#") or a simple
+  "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol
+  specifies a "must be used with" or a "must not be used with"
+  relationship, respectively.  If no rule is specified, then it is
+  assumed that the two packages are compatible and will function
+  either with or without each other.
+  
+\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
+  automatic differentiation options file to be used.  The file is
+  analogous to the ``optfile'' defined above but it specifies
+  information for the AD build process.
+  
+  The default file is located in {\em
+    tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
+  and "TAMC" compilers.  An alternate version is also available at
+  {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
+  "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}).
+  
+\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
+  soft-links and other bugs common with the \texttt{make} versions
+  provided by commercial Unix vendors, GNU \texttt{make} (sometimes
+  called \texttt{gmake}) should be preferred.  This option provides a
+  means for specifying the make executable to be used.
+  
+\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
+  machines, the ``bash'' shell is unavailable.  To run on these
+  systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
+  a Bourne, POSIX, or compatible) shell.  The syntax in these
+  circumstances is:
+  \begin{center}
+    \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
+  \end{center}
+  where \texttt{/bin/sh} can be replaced with the full path and name
+  of the desired shell.
+
+\end{description}
+
+
+\subsection{Building with MPI}
+\label{sect:mpi-build}
+
+Building MITgcm to use MPI libraries can be complicated due to the
+variety of different MPI implementations available, their dependencies
+or interactions with different compilers, and their often ad-hoc
+locations within file systems.  For these reasons, its generally a
+good idea to start by finding and reading the documentation for your
+machine(s) and, if necessary, seeking help from your local systems
+administrator.
+
+The steps for building MITgcm with MPI support are:
+\begin{enumerate}
+  
+\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:
+  \begin{rawhtml} <A
+    href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
+  \end{rawhtml}
+  \begin{center}
+    \texttt{MITgcm/tools/build\_options/}
+  \end{center}
+  \begin{rawhtml} </A> \end{rawhtml}
+  such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
+  \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
+  hand.  You may need help from your user guide or local systems
+  administrator to determine the exact location of the MPI libraries.
+  If libraries are not installed, MPI implementations and related
+  tools are available including:
+  \begin{itemize}
+  \item \begin{rawhtml} <A
+      href="http://www-unix.mcs.anl.gov/mpi/mpich/">
+    \end{rawhtml}
+    MPICH
+    \begin{rawhtml} </A> \end{rawhtml}
+
+  \item \begin{rawhtml} <A
+      href="http://www.lam-mpi.org/">
+    \end{rawhtml}
+    LAM/MPI
+    \begin{rawhtml} </A> \end{rawhtml}
+
+  \item \begin{rawhtml} <A
+      href="http://www.osc.edu/~pw/mpiexec/">
+    \end{rawhtml}
+    MPIexec
+    \begin{rawhtml} </A> \end{rawhtml}
+  \end{itemize}
+  
+\item Build the code with the \texttt{genmake2} \texttt{-mpi} option
+  (see Section \ref{sect:genmake}) using commands such as:
+{\footnotesize \begin{verbatim}
+  %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
+  %  make depend
+  %  make
+\end{verbatim} }
+  
+\item Run the code with the appropriate MPI ``run'' or ``exec''
+  program provided with your particular implementation of MPI.
+  Typical MPI packages such as MPICH will use something like:
+\begin{verbatim}
+  %  mpirun -np 4 -machinefile mf ./mitgcmuv
+\end{verbatim}
+  Sightly more complicated scripts may be needed for many machines
+  since execution of the code may be controlled by both the MPI
+  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/public/testing.html"> \end{rawhtml}regular
+  verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
+  at:
+  \begin{rawhtml} <A
+    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/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
+  \begin{rawhtml} </A> \end{rawhtml}
+
+\end{enumerate}
+
+An example of the above process on the MITgcm cluster (``cg01'') using
+the GNU g77 compiler and the mpich MPI library is:
+
+{\footnotesize \begin{verbatim}
+  %  cd MITgcm/verification/exp5
+  %  mkdir build
+  %  cd build
+  %  ../../../tools/genmake2 -mpi -mods=../code \
+       -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
+  %  make depend
+  %  make
+  %  cd ../input
+  %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
+       -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
+\end{verbatim} }
 
 \section[Running MITgcm]{Running the model in prognostic mode}
 \label{sect:runModel}
@@ -658,29 +855,29 @@
 written out, which is made of the following files:
 
 \begin{itemize}
-\item \texttt{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 \texttt{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 \texttt{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 \texttt{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 \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor
-(g/kg).
+\item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
+  vapor (g/kg).
 
-\item \texttt{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 \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.
+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:
 
@@ -703,42 +900,11 @@
 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://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}
-
+a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  
 
 \subsection{Looking at the output}
 
@@ -774,3 +940,37 @@
 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}
+
