/[MITgcm]/manual/s_getstarted/text/getting_started.tex

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-revision 1.35 by molod,
Thu Apr 20 22:09:08 2006 UTC
+revision 1.47 by jmc,
Tue Jan  9 01:02:48 2018 UTC
 Line 3
  %\section{Getting started}
- In this section, we describe how to use the model. In the first
+ We believe the best way to familiarize yourself with the
- section, we provide enough information to help you get started with
- the model. 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
+ found here as well as a brief description of the model structure
- directory and the case study examples.  The latter and the code
+ directory and the case study examples. Information is also provided
- structure are described more fully in chapters
+ here on how to customize the code when you are ready to try implementing
- \ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in
+ the configuration you have in mind.  The code and algorithm
- this section, we provide information on how to customize the code when
+ are described more fully in chapters \ref{chap:discretization} and
- you are ready to try implementing the configuration you have in mind.
+ \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:
+ There is a web-archived support mailing list for the model that
- \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
+ you can email at \texttt{MITgcm-support@mitgcm.org} after subscribing to:
+ \begin{rawhtml} <A href=http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
  \begin{verbatim}
- http://mitgcm.org/pelican
+ http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support/
  \end{verbatim}
  \begin{rawhtml} </A> \end{rawhtml}
- Here you will find an on-line version of this document, a
+ or browse at:
- ``browsable'' copy of the code and a searchable database of the model
+ \begin{rawhtml} <A href=http://mailman.mitgcm.org/pipermail/mitgcm-support/ target="idontexist"> \end{rawhtml}
- 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
- 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}
- http://mitgcm.org/mailman/listinfo/mitgcm-support/
+ http://mailman.mitgcm.org/pipermail/mitgcm-support/
- 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}
-Line 86 
 provide easy support for maintenance upd
+Line 68 
 provide easy support for maintenance upd
  \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
-Line 94 
 track of your changes. If CVS is not ava
+Line 76 
 track of your changes. If CVS is not ava
  download a tar file.
  Before you can use CVS, the following environment variable(s) should
  be set within your shell.  For a csh or tcsh shell, put the following
  \begin{verbatim}
  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
  \end{verbatim}
-Line 105 
 shells, put:
+Line 87 
 shells, put:
  \end{verbatim}
  in your \texttt{.profile} or \texttt{.bashrc} file.
  To get MITgcm through CVS, first register with the MITgcm CVS server
  using command:
  \begin{verbatim}
-Line 115 
 You only need to do a ``cvs login'' once
+Line 96 
 You only need to do a ``cvs login'' once
  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}
-Line 142 
 of CVS aliases
+Line 127 
 of CVS aliases
      \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline
      \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\
      \texttt{MITgcm\_verif\_basic}
      &  Source code plus a small set of the verification examples
      (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5},
      \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\
      \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\
      \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\
-Line 162 
 track of your file versions with respect
+Line 147 
 track of your file versions with respect
  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}
+ Note that it is possible to checkout code without ``cvs login'' and without
- \subsection{Method 2 - Tar file download}
+ setting any shell environment variables by specifying the pserver name and
- \label{sect:conventionalDownload}
+ password in one line, for example:
- 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/
+    %  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}
-Line 206 
 your copy instead of downloading the ent
+Line 176 
 your copy instead of downloading the ent
  \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
-Line 252 
 have run into a problem for which ``we h
+Line 222 
 have run into a problem for which ``we h
  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
-Line 262 
 that you may only have part of a patch.
+Line 232 
 that you may only have part of a patch.
  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: -->
-Line 286 
 structure).
+Line 276 
 structure).
  \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}.
  \item \texttt{pkg}: contains the source code for the packages. Each
    package corresponds to a subdirectory. For example, \texttt{gmredi}
    contains the code related to the Gent-McWilliams/Redi scheme,
    \texttt{aim} the code relative to the atmospheric intermediate
-   physics. The packages are described in detail in section 3.
+   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
    compute coefficients of the polynomial approximation to the knudsen
-Line 327 
 structure).
+Line 309 
 structure).
    \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
- \item \texttt{verification}: this directory contains the model
+   decompositions.
-   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}
+ \item \texttt{verification}: this directory contains the model
+   examples. See section \ref{sec:modelExamples}.
- \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{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
-   Suarez '94 forcing on the cubed sphere.
- \item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
-   Global Zonal Mean configuration, 1x64x5 resolution.
- \item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
-   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
- \item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
-   physics. 3D Equatorial Channel configuration.
- \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.
-   Global configuration, on latitude longitude grid with 128x64x5 grid
-   points ($2.8^\circ$ resolution).
- \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
-   latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
- \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
-   cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
-   resolution).
- \item \texttt{advect\_cs} Two-dimensional passive advection test on
-   cube sphere grid.
- \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
-   advection test on Cartesian grid.
- \item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
-   advection test on Cartesian grid.
- \item \texttt{carbon} Simple passive tracer experiment. Includes
-   derivative calculation. Described in detail in section
-   \ref{sect:eg-carbon-ad}.
- \item \texttt{flt\_example} Example of using float package.
- \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
-   boundary conditions and poles.
- \item \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:
+ \item \texttt{jobs}: contains sample job scripts for running MITgcm.
- \begin{itemize}
+ \item \texttt{lsopt}: Line search code used for optimization.
- \item \texttt{code}: contains the code particular to the example. At a
-   minimum, this directory includes the following files:
-   \begin{itemize}
+ \item \texttt{optim}: Interface between MITgcm and line search code.
-   \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}
+ \label{sec:buildingCode}
  \begin{rawhtml}
  <!-- CMIREDIR:buildingCode: -->
  \end{rawhtml}
-Line 515 
 To compile the code, we use the \texttt{
+Line 334 
 To compile the code, we use the \texttt{
  file (\texttt{Makefile}) that allows us to pre-process source files,
  specify compiler and optimization options and also figures out any
  file dependencies. We supply a script (\texttt{genmake2}), described
- in section \ref{sect:genmake}, that automatically creates the
+ in section \ref{sec:genmake}, that automatically creates the
  \texttt{Makefile} for you. You then need to build the dependencies and
  compile the code.
-Line 547 
 MITgcm.  In such cases, it is generally
+Line 366 
 MITgcm.  In such cases, it is generally
  Through the MITgcm-support list, the MITgcm developers are willing to
  provide help writing or modifing ``optfiles''.  And we encourage users
  to post new ``optfiles'' (particularly ones for new machines or
  architectures) to the
  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
  MITgcm-support@mitgcm.org
  \begin{rawhtml} </A> \end{rawhtml}
-Line 590 
 where the ``2'' can be replaced with a n
+Line 409 
 where the ``2'' can be replaced with a n
  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 by
+ 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/* .
-Line 604 
 where we are re-directing the stream of
+Line 423 
 where we are re-directing the stream of
  \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
-Line 706 
 the one experiment:
+Line 525 
 the one experiment:
  % ./mitgcmuv > output.txt
  \end{verbatim}
  \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
+ %Internally, \texttt{genmake2} determines the locations of needed
- files, the compiler, compiler options, libraries, and Unix tools.  It
+ %files, the compiler, compiler options, libraries, and Unix tools.  It
- relies upon a number of ``optfiles'' located in the
+ %relies upon a number of ``optfiles'' located in the
- \texttt{tools/build\_options} directory.
+ %\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
-Line 790 
 for inclusion.  Please send the file to
+Line 622 
 for inclusion.  Please send the file to
  \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:
-Line 799 
 obtained from:
+Line 633 
 obtained from:
  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
-Line 811 
 The most important command-line options
+Line 645 
 The most important command-line options
    (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
+ \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
-   set of packages to be used.  The normal order of precedence for
+   directories containing ``modifications''.  These directories contain
-   packages is as follows:
+   files with names that may (or may not) exist in the main MITgcm
-   \begin{enumerate}
+   source tree but will be overridden by any identically-named sources
-   \item If available, the command line (\texttt{--pdefault}) settings
+   within the ``MODS'' directories.
-     over-rule any others.
+   The order of precedence for this "name-hiding" is as follows:
-   \item Next, \texttt{genmake2} will look for a file named
+   \begin{itemize}
-     ``\texttt{packages.conf}'' in the local directory or in any of the
+   \item ``MODS'' directories (in the order given)
-     directories specified with the \texttt{--mods} option.
+   \item Packages either explicitly specified or provided by default
+     (in the order given)
-   \item Finally, if neither of the above are available,
+   \item Packages included due to package dependencies (in the order
-     \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
+     that that package dependencies are parsed)
-   \end{enumerate}
+   \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.
    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
-Line 838 
 The most important command-line options
+Line 682 
 The most important command-line options
    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}).
+   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
    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,
-Line 891 
 The most important command-line options
+Line 718 
 The most important command-line options
  \end{description}
  \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
-Line 905 
 administrator.
+Line 731 
 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:
+   \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/}
-Line 941 
 The steps for building MITgcm with MPI s
+Line 767 
 The steps for building MITgcm with MPI s
      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:
+   (see Section \ref{sec: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:
-Line 961 
 The steps for building MITgcm with MPI s
+Line 787 
 The steps for building MITgcm with MPI s
    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}
-Line 990 
 the GNU g77 compiler and the mpich MPI l
+Line 823 
 the GNU g77 compiler and the mpich MPI l
  \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 succesfully (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.
-Line 1023 
 output is kept in \texttt{results/output
+Line 856 
 output is kept in \texttt{results/output
  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 and, when using \texttt{mnc},
-Line 1034 
 both as determined by \texttt{code/packa
+Line 865 
 both as determined by \texttt{code/packa
  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}
-Line 1082 
 there is an additional ``pickup'' file:
+Line 912 
 there is an additional ``pickup'' file:
  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
  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
  used to restart the model but are overwritten every other time they are
  output to save disk space during long integrations.
  \subsubsection{MNC output files}
  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
  is usually (though not necessarily) placed within a subdirectory with
- a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files
+ a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.
- within this subdirectory are all in the ``self-describing'' netCDF
- format and can thus be browsed and/or plotted using tools such as:
- \begin{itemize}
- \item \texttt{ncdump} is a utility which is typically included
-   with every netCDF install:
-   \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
- \begin{verbatim}
- http://www.unidata.ucar.edu/packages/netcdf/
- \end{verbatim}
-   \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
-   binaries into formatted ASCII text files.
- \item \texttt{ncview} utility is a very convenient and quick way
-   to plot netCDF data and it runs on most OSes:
-   \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
- \begin{verbatim}
- http://meteora.ucsd.edu/~pierce/ncview_home_page.html
- \end{verbatim}
-   \begin{rawhtml} </A> \end{rawhtml}
- \item MatLAB(c) and other common post-processing environments provide
-   various netCDF interfaces including:
-   \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
- \begin{verbatim}
- http://mexcdf.sourceforge.net/
- \end{verbatim}
-   \begin{rawhtml} </A> \end{rawhtml}
-   \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
- \begin{verbatim}
- http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
- \end{verbatim}
-   \begin{rawhtml} </A> \end{rawhtml}
- \end{itemize}
  \subsection{Looking at the output}
-Line 1163 
 Some examples of reading and visualizing
+Line 957 
 Some examples of reading and visualizing
  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}

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