--- manual/s_getstarted/text/getting_started.tex	2005/08/09 21:52:09	1.31
+++ manual/s_getstarted/text/getting_started.tex	2006/06/28 17:20:51	1.38
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.31 2005/08/09 21:52:09 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.38 2006/06/28 17:20:51 molod Exp $
 % $Name:  $
 
 %\section{Getting started}
@@ -15,25 +15,13 @@
 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 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 +29,6 @@
 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 +104,7 @@
 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{verbatim}
 http://mitgcm.org/source_code.html
 \end{verbatim}
@@ -163,7 +141,7 @@
 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/usingcvstoget.html" target="idontexist"> \end{rawhtml}
 here
 \begin{rawhtml} </A> \end{rawhtml} 
 .
@@ -176,27 +154,6 @@
    %  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 +220,26 @@
 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 +264,12 @@
 
 \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 +278,17 @@
   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 +297,21 @@
   \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 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{jobs}: contains sample job scripts for running MITgcm.
   
-\item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
-  Suarez '94 forcing.
+\item \texttt{lsopt}: Line search code used for optimization.
   
-\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 ($2.8^\circ{\rm degree}$ 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{optim}: Interface between MITgcm and line search code.
   
-\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 +355,7 @@
 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 +409,392 @@
 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/cgi-bin/viewcvs.cgi/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/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/">
+  \end{rawhtml}
+  {\footnotesize \tt
+    http://mitgcm.org/cgi-bin/viewcvs.cgi/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 +849,29 @@
 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 +894,11 @@
 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 +934,37 @@
 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}
+
