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

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-revision 1.17 by edhill,
Thu Jan 29 15:11:39 2004 UTC
+revision 1.45 by jmc,
Wed May 11 18:58:02 2011 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}
- \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
  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}
-Line 37 
 http://mitgcm.org/mailman/listinfo/mitgc
+Line 27 
 http://mitgcm.org/mailman/listinfo/mitgc
  http://mitgcm.org/pipermail/mitgcm-support/
  \end{verbatim}
  \begin{rawhtml} </A> \end{rawhtml}
- Essentially all of the MITgcm web pages can be searched using a
- popular web crawler such as Google or through our own search facility:
- \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}
- \begin{verbatim}
- http://mitgcm.org/htdig/
- \end{verbatim}
- \begin{rawhtml} </A> \end{rawhtml}
- %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
  \section{Obtaining the code}
- \label{sect:obtainingCode}
+ \label{sec:obtainingCode}
+ \begin{rawhtml}
+ <!-- CMIREDIR:obtainingCode: -->
+ \end{rawhtml}
  MITgcm can be downloaded from our system by following
  the instructions below. As a courtesy we ask that you send e-mail to us at
-Line 79 
 provide easy support for maintenance upd
+Line 62 
 provide easy support for maintenance upd
  \end{enumerate}
+ \subsection{Method 1 - Checkout from CVS}
+ \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
  track of your changes. If CVS is not available on your machine, you can also
-Line 89 
 be set within your shell.  For a csh or
+Line 75 
 be set within your shell.  For a csh or
  \begin{verbatim}
  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
  \end{verbatim}
- in your .cshrc or .tcshrc file.  For bash or sh shells, put:
+ in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
+ shells, put:
  \begin{verbatim}
  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
  \end{verbatim}
- in your .profile or .bashrc file.
+ in your \texttt{.profile} or \texttt{.bashrc} file.
  To get MITgcm through CVS, first register with the MITgcm CVS server
-Line 105 
 You only need to do a ``cvs login'' once
+Line 92 
 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}
+ As a convenience, the MITgcm CVS server contains aliases which are
+ named subsets of the codebase.  These aliases can be especially
+ helpful when used over slow internet connections or on machines with
+ restricted storage space.  Table \ref{tab:cvsModules} contains a list
+ of CVS aliases
+ \begin{table}[htb]
+   \centering
+   \begin{tabular}[htb]{|lp{3.25in}|}\hline
+     \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline
+     \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\
+     \texttt{MITgcm\_verif\_basic}
+     &  Source code plus a small set of the verification examples
+     (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5},
+     \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\
+     \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\
+     \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\
+     \texttt{MITgcm\_verif\_all}    &  Source code plus all of the
+     verification examples. \\\hline
+   \end{tabular}
+   \caption{MITgcm CVS Modules}
+   \label{tab:cvsModules}
+ \end{table}
- The checkout process creates a directory called \textit{MITgcm}. If
+ The checkout process creates a directory called \texttt{MITgcm}. If
- the directory \textit{MITgcm} exists this command updates your code
+ the directory \texttt{MITgcm} exists this command updates your code
  based on the repository. Each directory in the source tree contains a
- directory \textit{CVS}. This information is required by CVS to keep
+ directory \texttt{CVS}. This information is required by CVS to keep
  track of your file versions with respect to the repository. Don't edit
- the files in \textit{CVS}!  You can also use CVS to download code
+ the files in \texttt{CVS}!  You can also use CVS to download code
  updates.  More extensive information on using CVS for maintaining
  MITgcm code can be found
- \begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml}
+ \begin{rawhtml} <A href="http://mitgcm.org/public/using_cvs.html" target="idontexist"> \end{rawhtml}
  here
  \begin{rawhtml} </A> \end{rawhtml}
  .
+ It is important to note that the CVS aliases in Table
+ \ref{tab:cvsModules} cannot be used in conjunction with the CVS
- \paragraph*{Conventional download method}
+ \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
- \label{sect:conventionalDownload}
+ they create can be changed to a different name following the check-out:
- 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 co -P MITgcm_verif_basic
+    %  mv MITgcm MITgcm_verif_basic
  \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.
- \paragraph*{Upgrading from an earlier version}
+ \subsubsection{Upgrading from an earlier version}
  If you already have an earlier version of the code you can ``upgrade''
  your copy instead of downloading the entire repository again. First,
 Line 166 
 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 212 
 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 222 
 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: -->
+ \end{rawhtml}
  The ``numerical'' model is contained within a execution environment
  support wrapper. This wrapper is designed to provide a general
-Line 230 
 framework for grid-point models. MITgcmU
+Line 253 
 framework for grid-point models. MITgcmU
  model that uses the framework. Under this structure the model is split
  into execution environment support code and conventional numerical
  model code. The execution environment support code is held under the
- \textit{eesupp} directory. The grid point model code is held under the
+ \texttt{eesupp} directory. The grid point model code is held under the
- \textit{model} directory. Code execution actually starts in the
+ \texttt{model} directory. Code execution actually starts in the
- \textit{eesupp} routines and not in the \textit{model} routines. For
+ \texttt{eesupp} routines and not in the \texttt{model} routines. For
- this reason the top-level \textit{MAIN.F} is in the
+ this reason the top-level \texttt{MAIN.F} is in the
- \textit{eesupp/src} directory. In general, end-users should not need
+ \texttt{eesupp/src} directory. In general, end-users should not need
  to worry about this level. The top-level routine for the numerical
- part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is
+ part of the code is in \texttt{model/src/THE\_MODEL\_MAIN.F}. Here is
  a brief description of the directory structure of the model under the
  root tree (a detailed description is given in section 3: Code
  structure).
  \begin{itemize}
- \item \textit{bin}: this directory is initially empty. It is the
+ \item \texttt{doc}: contains brief documentation notes.
-   default directory in which to compile the code.
- \item \textit{diags}: contains the code relative to time-averaged
-   diagnostics. It is subdivided into two subdirectories \textit{inc}
-   and \textit{src} that contain include files (*.\textit{h} files) and
-   Fortran subroutines (*.\textit{F} files), respectively.
- \item \textit{doc}: contains brief documentation notes.
- \item \textit{eesupp}: contains the execution environment source code.
-   Also subdivided into two subdirectories \textit{inc} and
-   \textit{src}.
- \item \textit{exe}: this directory is initially empty. It is the
-   default directory in which to execute the code.
- \item \textit{model}: this directory contains the main source code.
+ \item \texttt{eesupp}: contains the execution environment source code.
-   Also subdivided into two subdirectories \textit{inc} and
+   Also subdivided into two subdirectories \texttt{inc} and
-   \textit{src}.
+   \texttt{src}.
+ \item \texttt{model}: this directory contains the main source code.
+   Also subdivided into two subdirectories \texttt{inc} and
+   \texttt{src}.
- \item \textit{pkg}: contains the source code for the packages. Each
+ \item \texttt{pkg}: contains the source code for the packages. Each
-   package corresponds to a subdirectory. For example, \textit{gmredi}
+   package corresponds to a subdirectory. For example, \texttt{gmredi}
    contains the code related to the Gent-McWilliams/Redi scheme,
-   \textit{aim} the code relative to the atmospheric intermediate
+   \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 \textit{tools}: this directory contains various useful tools.
+ \item \texttt{tools}: this directory contains various useful tools.
-   For example, \textit{genmake2} is a script written in csh (C-shell)
+   For example, \texttt{genmake2} is a script written in csh (C-shell)
    that should be used to generate your makefile. The directory
-   \textit{adjoint} contains the makefile specific to the Tangent
+   \texttt{adjoint} contains the makefile specific to the Tangent
    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
-   The latter is described in details in part V.
+   The latter is described in detail in part \ref{chap.ecco}.
+   This directory also contains the subdirectory build\_options, which
+   contains the `optfiles' with the compiler options for the different
+   compilers and machines that can run MITgcm.
- \item \textit{utils}: this directory contains various utilities. The
+ \item \texttt{utils}: this directory contains various utilities. The
-   subdirectory \textit{knudsen2} contains code and a makefile that
+   subdirectory \texttt{knudsen2} contains code and a makefile that
    compute coefficients of the polynomial approximation to the knudsen
    formula for an ocean nonlinear equation of state. The
-   \textit{matlab} subdirectory contains matlab scripts for reading
+   \texttt{matlab} subdirectory contains matlab scripts for reading
-   model output directly into matlab. \textit{scripts} contains C-shell
+   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 \textit{verification}: this directory contains the model
+ \item \texttt{verification}: this directory contains the model
-   examples. See section \ref{sect:modelExamples}.
+   examples. See section \ref{sec:modelExamples}.
- \end{itemize}
- \section{Example experiments}
- \label{sect:modelExamples}
- %% a set of twenty-four pre-configured numerical experiments
+ \item \texttt{jobs}: contains sample job scripts for running MITgcm.
- The MITgcm distribution comes with more than a dozen pre-configured
- numerical experiments. Some of these example experiments are tests of
- individual parts of the model code, but many are fully fledged
- numerical simulations. A few of the examples are used for tutorial
- documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.
- The other examples follow the same general structure as the tutorial
- examples. However, they only include brief instructions in a text file
- called {\it README}.  The examples are located in subdirectories under
- the directory \textit{verification}. Each example is briefly described
- below.
- \subsection{Full list of model examples}
- \begin{enumerate}
- \item \textit{exp0} - single layer, ocean double gyre (barotropic with
-   free-surface). This experiment is described in detail in section
-   \ref{sect:eg-baro}.
- \item \textit{exp1} - Four layer, ocean double gyre. This experiment
-   is described in detail in section \ref{sect:eg-baroc}.
- \item \textit{exp2} - 4x4 degree global ocean simulation with steady
-   climatological forcing. This experiment is described in detail in
-   section \ref{sect:eg-global}.
- \item \textit{exp4} - Flow over a Gaussian bump in open-water or
-   channel with open boundaries.
- \item \textit{exp5} - Inhomogenously forced ocean convection in a
-   doubly periodic box.
- \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
- Gent/McWilliams scheme). 2D (Y-Z).
- \item \textit{internal wave} - Ocean internal wave forced by open
-   boundary conditions.
- \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
-   scheme; 1 month integration
- \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and
-   Suarez '94 forcing.
- \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
-   Suarez '94 forcing.
- \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
-   Suarez '94 forcing on the cubed sphere.
- \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
-   Global Zonal Mean configuration, 1x64x5 resolution.
- \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
-   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
- \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
-   physics. 3D Equatorial Channel configuration.
- \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
-   Global configuration, on latitude longitude grid with 128x64x5 grid
-   points ($2.8^\circ{\rm degree}$ resolution).
- \item \textit{adjustment.128x64x1} Barotropic adjustment problem on
-   latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
-     degree}$ resolution).
- \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on
-   cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
-     degree}$ resolution).
- \item \textit{advect\_cs} Two-dimensional passive advection test on
-   cube sphere grid.
- \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive
-   advection test on Cartesian grid.
- \item \textit{advect\_yz} Two-dimensional (vertical plane) passive
-   advection test on Cartesian grid.
- \item \textit{carbon} Simple passive tracer experiment. Includes
+ \item \texttt{lsopt}: Line search code used for optimization.
-   derivative calculation. Described in detail in section
-   \ref{sect:eg-carbon-ad}.
- \item \textit{flt\_example} Example of using float package.
- \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux
-   boundary conditions and poles.
- \item \textit{global\_ocean\_pressure} Global circulation in pressure
-   coordinate (non-Boussinesq ocean model). Described in detail in
-   section \ref{sect:eg-globalpressure}.
- \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube
-   sphere grid.
- \end{enumerate}
- \subsection{Directory structure of model examples}
- Each example directory has the following subdirectories:
- \begin{itemize}
- \item \textit{code}: contains the code particular to the example. At a
-   minimum, this directory includes the following files:
-   \begin{itemize}
-   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
-     the ``execution environment'' part of the code. The default
-     version is located in \textit{eesupp/inc}.
-   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
-     the ``numerical model'' part of the code. The default version is
-     located in \textit{model/inc}.
-   \item \textit{code/SIZE.h}: declares size of underlying
-     computational grid.  The default version is located in
-     \textit{model/inc}.
-   \end{itemize}
-   In addition, other include files and subroutines might be present in
-   \textit{code} depending on the particular experiment. See Section 2
-   for more details.
- \item \textit{input}: contains the input data files required to run
-   the example. At a minimum, the \textit{input} directory contains the
-   following files:
-   \begin{itemize}
-   \item \textit{input/data}: this file, written as a namelist,
-     specifies the main parameters for the experiment.
-   \item \textit{input/data.pkg}: contains parameters relative to the
-     packages used in the experiment.
-   \item \textit{input/eedata}: this file contains ``execution
+ \item \texttt{optim}: Interface between MITgcm and line search code.
-     environment'' data. At present, this consists of a specification
-     of the number of threads to use in $X$ and $Y$ under multithreaded
-     execution.
-   \end{itemize}
-   In addition, you will also find in this directory the forcing and
-   topography files as well as the files describing the initial state
-   of the experiment.  This varies from experiment to experiment. See
-   section 2 for more details.
- \item \textit{results}: this directory contains the output file
-   \textit{output.txt} produced by the simulation example. This file is
-   useful for comparison with your own output when you run the
-   experiment.
  \end{itemize}
- Once you have chosen the example you want to run, you are ready to
+ \section[Building MITgcm]{Building the code}
+ \label{sec:buildingCode}
+ \begin{rawhtml}
+ <!-- CMIREDIR:buildingCode: -->
+ \end{rawhtml}
+ To compile the code, we use the \texttt{make} program. This uses a
+ file (\texttt{Makefile}) that allows us to pre-process source files,
+ specify compiler and optimization options and also figures out any
+ file dependencies. We supply a script (\texttt{genmake2}), described
+ in section \ref{sec:genmake}, that automatically creates the
+ \texttt{Makefile} for you. You then need to build the dependencies and
  compile the code.
- \section{Building the code}
+ As an example, assume that you want to build and run experiment
- \label{sect:buildingCode}
+ \texttt{verification/exp2}. The are multiple ways and places to
- To compile the code, we use the {\em make} program. This uses a file
- ({\em Makefile}) that allows us to pre-process source files, specify
- compiler and optimization options and also figures out any file
- dependencies. We supply a script ({\em genmake2}), described in
- section \ref{sect:genmake}, that automatically creates the {\em
-   Makefile} for you. You then need to build the dependencies and
- compile the code.
- As an example, let's assume that you want to build and run experiment
- \textit{verification/exp2}. The are multiple ways and places to
  actually do this but here let's build the code in
- \textit{verification/exp2/input}:
+ \texttt{verification/exp2/build}:
  \begin{verbatim}
- % cd verification/exp2/input
+ % cd verification/exp2/build
  \end{verbatim}
- First, build the {\em Makefile}:
+ First, build the \texttt{Makefile}:
  \begin{verbatim}
  % ../../../tools/genmake2 -mods=../code
  \end{verbatim}
- The command line option tells {\em genmake} to override model source
+ The command line option tells \texttt{genmake} to override model source
- code with any files in the directory {\em ./code/}.
+ code with any files in the directory \texttt{../code/}.
- On many systems, the {\em genmake2} program will be able to
+ On many systems, the \texttt{genmake2} program will be able to
  automatically recognize the hardware, find compilers and other tools
- within the user's path (``echo \$PATH''), and then choose an
+ within the user's path (``\texttt{echo \$PATH}''), and then choose an
- appropriate set of options from the files contained in the {\em
+ appropriate set of options from the files (``optfiles'') contained in
-   tools/build\_options} directory.  Under some circumstances, a user
+ the \texttt{tools/build\_options} directory.  Under some
- may have to create a new ``optfile'' in order to specify the exact
+ circumstances, a user may have to create a new ``optfile'' in order to
- combination of compiler, compiler flags, libraries, and other options
+ specify the exact combination of compiler, compiler flags, libraries,
- necessary to build a particular configuration of MITgcm.  In such
+ and other options necessary to build a particular configuration of
- cases, it is generally helpful to read the existing ``optfiles'' and
+ MITgcm.  In such cases, it is generally helpful to read the existing
- mimic their syntax.
+ ``optfiles'' and mimic their syntax.
  Through the MITgcm-support list, the MITgcm developers are willing to
  provide help writing or modifing ``optfiles''.  And we encourage users
  to post new ``optfiles'' (particularly ones for new machines or
  architectures) to the
- \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
+ \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
  MITgcm-support@mitgcm.org
  \begin{rawhtml} </A> \end{rawhtml}
  list.
- To specify an optfile to {\em genmake2}, the syntax is:
+ To specify an optfile to \texttt{genmake2}, the syntax is:
  \begin{verbatim}
  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
  \end{verbatim}
- Once a {\em Makefile} has been generated, we create the dependencies:
+ Once a \texttt{Makefile} has been generated, we create the
+ dependencies with the command:
  \begin{verbatim}
  % make depend
  \end{verbatim}
- This modifies the {\em Makefile} by attaching a [long] list of files
+ This modifies the \texttt{Makefile} by attaching a (usually, long)
- upon which other files depend. The purpose of this is to reduce
+ list of files upon which other files depend. The purpose of this is to
- re-compilation if and when you start to modify the code. The {\tt make
+ reduce re-compilation if and when you start to modify the code. The
-   depend} command also creates links from the model source to this
+ {\tt make depend} command also creates links from the model source to
- directory.
+ this directory.  It is important to note that the {\tt make depend}
+ stage will occasionally produce warnings or errors since the
+ dependency parsing tool is unable to find all of the necessary header
+ files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
+ is usually OK to ignore the warnings/errors and proceed to the next
+ step.
- Next compile the code:
+ Next one can compile the code using:
  \begin{verbatim}
  % make
  \end{verbatim}
- The {\tt make} command creates an executable called \textit{mitgcmuv}.
+ The {\tt make} command creates an executable called \texttt{mitgcmuv}.
  Additional make ``targets'' are defined within the makefile to aid in
- the production of adjoint and other versions of MITgcm.
+ the production of adjoint and other versions of MITgcm.  On SMP
+ (shared multi-processor) systems, the build process can often be sped
+ up appreciably using the command:
+ \begin{verbatim}
+ % make -j 2
+ \end{verbatim}
+ where the ``2'' can be replaced with a number that corresponds to the
+ number of CPUs available.
  Now you are ready to run the model. General instructions for doing so are
- given in section \ref{sect:runModel}. Here, we can run the model with:
+ given in section \ref{sec:runModel}. Here, we can run the model by
+ first creating links to all the input files:
+ \begin{verbatim}
+ ln -s ../input/* .
+ \end{verbatim}
+ and then calling the executable with:
  \begin{verbatim}
  ./mitgcmuv > output.txt
  \end{verbatim}
- where we are re-directing the stream of text output to the file {\em
+ where we are re-directing the stream of text output to the file
- output.txt}.
+ \texttt{output.txt}.
  \subsection{Building/compiling the code elsewhere}
- In the example above (section \ref{sect:buildingCode}) we built the
+ In the example above (section \ref{sec:buildingCode}) we built the
  executable in the {\em input} directory of the experiment for
  convenience. You can also configure and compile the code in other
  locations, for example on a scratch disk with out having to copy the
-Line 633 
 the one experiment:
+Line 516 
 the one experiment:
  \end{verbatim}
+ \subsection{Using \texttt{genmake2}}
- \subsection{Using \textit{genmake2}}
+ \label{sec:genmake}
- \label{sect:genmake}
  To compile the code, first use the program \texttt{genmake2} (located
- in the \textit{tools} directory) to generate a Makefile.
+ 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 {\em
+ %relies upon a number of ``optfiles'' located in the
-   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 717 
 for inclusion.  Please send the file to
+Line 613 
 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 739 
 The most important command-line options
+Line 637 
 The most important command-line options
    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{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
+   directories containing ``modifications''.  These directories contain
+   files with names that may (or may not) exist in the main MITgcm
+   source tree but will be overridden by any identically-named sources
+   within the ``MODS'' directories.
+   The order of precedence for this "name-hiding" is as follows:
+   \begin{itemize}
+   \item ``MODS'' directories (in the order given)
+   \item Packages either explicitly specified or provided by default
+     (in the order given)
+   \item Packages included due to package dependencies (in the order
+     that that package dependencies are parsed)
+   \item The "standard dirs" (which may have been specified by the
+     ``-standarddirs'' option)
+   \end{itemize}
+ \item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
+   where package groups are defined. If not set, the package-groups
+   definition will be read from {\em pkg/pkg\_groups}.
+   It also contains the default list of packages (defined
+   as the group ``{\it default\_pkg\_list}'' which is used
+   when no specific package list ({\em packages.conf})
+   is found in current directory or in any "MODS" directory.
  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
    used for packages.
-Line 751 
 The most important command-line options
+Line 674 
 The most important command-line options
    assumed that the two packages are compatible and will function
    either with or without each other.
- \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
-   set of packages to be used.
-   If not set, the default package list will be read from {\em
-     pkg/pkg\_default}
  \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
-Line 769 
 The most important command-line options
+Line 686 
 The most important command-line options
    "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
+ \item[\texttt{--mpi}] This option enables certain MPI features (using
-   directories containing ``modifications''.  These directories contain
+   CPP \texttt{\#define}s) within the code and is necessary for MPI
-   files with names that may (or may not) exist in the main MITgcm
+   builds (see Section \ref{sec:mpi-build}).
-   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{--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{sec: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{sec: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{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:
+ \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}
- \section{Running the model}
+ An example of the above process on the MITgcm cluster (``cg01'') using
- \label{sect:runModel}
+ the GNU g77 compiler and the mpich MPI library is:
- If compilation finished succesfuully (section \ref{sect:buildModel})
+ {\footnotesize \begin{verbatim}
- then an executable called {\em mitgcmuv} will now exist in the local
+   %  cd MITgcm/verification/exp5
- directory.
+   %  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{sec:runModel}
+ \begin{rawhtml}
+ <!-- CMIREDIR:runModel: -->
+ \end{rawhtml}
+ If compilation finished succesfully (section \ref{sec:buildingCode})
+ then an executable called \texttt{mitgcmuv} will now exist in the
+ local directory.
- To run the model as a single process (ie. not in parallel) simply
+ To run the model as a single process (\textit{ie.} not in parallel)
- type:
+ simply type:
  \begin{verbatim}
  % ./mitgcmuv
  \end{verbatim}
-Line 814 
 do!). The above command will spew out ma
+Line 835 
 do!). The above command will spew out ma
  your screen.  This output contains details such as parameter values as
  well as diagnostics such as mean Kinetic energy, largest CFL number,
  etc. It is worth keeping this text output with the binary output so we
- normally re-direct the {\em stdout} stream as follows:
+ normally re-direct the \texttt{stdout} stream as follows:
  \begin{verbatim}
  % ./mitgcmuv > output.txt
  \end{verbatim}
+ In the event that the model encounters an error and stops, it is very
- For the example experiments in {\em verification}, an example of the
+ helpful to include the last few line of this \texttt{output.txt} file
- output is kept in {\em results/output.txt} for comparison. You can compare
+ along with the (\texttt{stderr}) error message within any bug reports.
- your {\em output.txt} with this one to check that the set-up works.
+ For the example experiments in \texttt{verification}, an example of the
+ output is kept in \texttt{results/output.txt} for comparison. You can
+ compare your \texttt{output.txt} with the corresponding one for that
+ experiment to check that the set-up works.
  \subsection{Output files}
- The model produces various output files. At a minimum, the instantaneous
+ The model produces various output files and, when using \texttt{mnc},
- ``state'' of the model is written out, which is made of the following files:
+ sometimes even directories.  Depending upon the I/O package(s)
+ selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
+ both as determined by \texttt{code/packages.conf}) and the run-time
+ flags set (in \texttt{input/data.pkg}), the following output may
+ appear.
+ \subsubsection{MDSIO output files}
+ The ``traditional'' output files are generated by the \texttt{mdsio}
+ package.  At a minimum, the instantaneous ``state'' of the model is
+ written out, which is made of the following files:
  \begin{itemize}
- \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>
+ \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
-$ eastward).
+   and positive eastward).
- \item \textit{V.00000nIter} - meridional component of velocity field (m/s
+ \item \texttt{V.00000nIter} - meridional component of velocity field
- and $> 0$ northward).
+   (m/s and positive northward).
- \item \textit{W.00000nIter} - vertical component of velocity field (ocean:
+ \item \texttt{W.00000nIter} - vertical component of velocity field
- m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure
+   (ocean: m/s and positive upward, atmosphere: Pa/s and positive
- i.e. downward).
+   towards increasing pressure i.e. downward).
- \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,
+ \item \texttt{T.00000nIter} - potential temperature (ocean:
- atmosphere: $^{0}$K).
+   $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
- \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor
+ \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
- (g/kg).
+   vapor (g/kg).
- \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:
+ \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
- surface pressure anomaly (Pa).
+   atmosphere: surface pressure anomaly (Pa).
  \end{itemize}
- The chain \textit{00000nIter} consists of ten figures that specify the
+ The chain \texttt{00000nIter} consists of ten figures that specify the
- iteration number at which the output is written out. For example, \textit{%
+ iteration number at which the output is written out. For example,
- U.0000000300} is the zonal velocity at iteration 300.
+ \texttt{U.0000000300} is the zonal velocity at iteration 300.
  In addition, a ``pickup'' or ``checkpoint'' file called:
  \begin{itemize}
- \item \textit{pickup.00000nIter}
+ \item \texttt{pickup.00000nIter}
  \end{itemize}
  is written out. This file represents the state of the model in a condensed
-Line 866 
 form and is used for restarting the inte
+Line 902 
 form and is used for restarting the inte
  there is an additional ``pickup'' file:
  \begin{itemize}
- \item \textit{pickup\_cd.00000nIter}
+ \item \texttt{pickup\_cd.00000nIter}
  \end{itemize}
  containing the D-grid velocity data and that has to be written out as well
  in order to restart the integration. Rolling checkpoint files are the same
  as the pickup files but are named differently. Their name contain the chain
- \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be
+ \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
  used to restart the model but are overwritten every other time they are
  output to save disk space during long integrations.
+ \subsubsection{MNC output files}
+ Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
+ is usually (though not necessarily) placed within a subdirectory with
+ a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.
  \subsection{Looking at the output}
- All the model data are written according to a ``meta/data'' file format.
+ The ``traditional'' or mdsio model data are written according to a
- Each variable is associated with two files with suffix names \textit{.data}
+ ``meta/data'' file format.  Each variable is associated with two files
- and \textit{.meta}. The \textit{.data} file contains the data written in
+ with suffix names \texttt{.data} and \texttt{.meta}. The
- binary form (big\_endian by default). The \textit{.meta} file is a
+ \texttt{.data} file contains the data written in binary form
- ``header'' file that contains information about the size and the structure
+ (big\_endian by default). The \texttt{.meta} file is a ``header'' file
- of the \textit{.data} file. This way of organizing the output is
+ that contains information about the size and the structure of the
- particularly useful when running multi-processors calculations. The base
+ \texttt{.data} file. This way of organizing the output is particularly
- version of the model includes a few matlab utilities to read output files
+ useful when running multi-processors calculations. The base version of
- written in this format. The matlab scripts are located in the directory
+ the model includes a few matlab utilities to read output files written
- \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads
+ in this format. The matlab scripts are located in the directory
- the data. Look at the comments inside the script to see how to use it.
+ \texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m}
+ reads the data. Look at the comments inside the script to see how to
+ use it.
  Some examples of reading and visualizing some output in {\em Matlab}:
  \begin{verbatim}
-Line 905 
 Some examples of reading and visualizing
+Line 949 
 Some examples of reading and visualizing
  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
  \end{verbatim}
- \section{Doing it yourself: customizing the code}
+ Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
+ they are described in Section \ref{sec:pkg:mnc}.
- When you are ready to run the model in the configuration you want, the
- easiest thing is to use and adapt the setup of the case studies
- experiment (described previously) that is the closest to your
- configuration. Then, the amount of setup will be minimized. In this
- section, we focus on the setup relative to the ``numerical model''
- part of the code (the setup relative to the ``execution environment''
- part is covered in the parallel implementation section) and on the
- variables and parameters that you are likely to change.
- \subsection{Configuration and setup}
- The CPP keys relative to the ``numerical model'' part of the code are
- all defined and set in the file \textit{CPP\_OPTIONS.h }in the
- directory \textit{ model/inc }or in one of the \textit{code
- }directories of the case study experiments under
- \textit{verification.} The model parameters are defined and declared
- in the file \textit{model/inc/PARAMS.h }and their default values are
- set in the routine \textit{model/src/set\_defaults.F. }The default
- values can be modified in the namelist file \textit{data }which needs
- to be located in the directory where you will run the model. The
- parameters are initialized in the routine
- \textit{model/src/ini\_parms.F}.  Look at this routine to see in what
- part of the namelist the parameters are located.
- In what follows the parameters are grouped into categories related to
- the computational domain, the equations solved in the model, and the
- simulation controls.
- \subsection{Computational domain, geometry and time-discretization}
- \begin{description}
- \item[dimensions] \
-   The number of points in the x, y,\textit{\ }and r\textit{\
-   }directions are represented by the variables \textbf{sNx}\textit{,
-   }\textbf{sNy}\textit{, } and \textbf{Nr}\textit{\ }respectively
-   which are declared and set in the file \textit{model/inc/SIZE.h.
-   }(Again, this assumes a mono-processor calculation. For
-   multiprocessor calculations see section on parallel implementation.)
- \item[grid] \
-   Three different grids are available: cartesian, spherical polar, and
-   curvilinear (including the cubed sphere). The grid is set through
-   the logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{
-     usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{
-     usingCurvilinearGrid}\textit{. }In the case of spherical and
-   curvilinear grids, the southern boundary is defined through the
-   variable \textbf{phiMin} \textit{\ }which corresponds to the
-   latitude of the southern most cell face (in degrees). The resolution
-   along the x and y directions is controlled by the 1D arrays
-   \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters in
-   the case of a cartesian grid, in degrees otherwise). The vertical
-   grid spacing is set through the 1D array \textbf{delz }for the ocean
-   (in meters) or \textbf{delp}\textit{\ }for the atmosphere (in Pa).
-   The variable \textbf{ Ro\_SeaLevel} represents the standard position
-   of Sea-Level in ''R'' coordinate. This is typically set to 0m for
-   the ocean (default value) and 10$ ^{5}$Pa for the atmosphere. For
-   the atmosphere, also set the logical variable \textbf{groundAtK1} to
-   '.\texttt{TRUE}.'. which put the first level (k=1) at the lower
-   boundary (ground).
-   For the cartesian grid case, the Coriolis parameter $f$ is set
-   through the variables \textbf{f0}\textit{\ }and
-   \textbf{beta}\textit{\ }which correspond to the reference Coriolis
-   parameter (in s$^{-1}$) and $\frac{\partial f}{ \partial y}$(in
-   m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ } is set
-   to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
-   southern edge of the domain.
- \item[topography - full and partial cells] \
-   The domain bathymetry is read from a file that contains a 2D (x,y)
-   map of depths (in m) for the ocean or pressures (in Pa) for the
-   atmosphere. The file name is represented by the variable
-   \textbf{bathyFile}\textit{. }The file is assumed to contain binary
-   numbers giving the depth (pressure) of the model at each grid cell,
-   ordered with the x coordinate varying fastest. The points are
-   ordered from low coordinate to high coordinate for both axes. The
-   model code applies without modification to enclosed, periodic, and
-   double periodic domains. Periodicity is assumed by default and is
-   suppressed by setting the depths to 0m for the cells at the limits
-   of the computational domain (note: not sure this is the case for the
-   atmosphere). The precision with which to read the binary data is
-   controlled by the integer variable \textbf{readBinaryPrec }which can
-   take the value \texttt{32} (single precision) or \texttt{64} (double
-   precision). See the matlab program \textit{ gendata.m }in the
-   \textit{input }directories under \textit{verification }to see how
-   the bathymetry files are generated for the case study experiments.
-   To use the partial cell capability, the variable
-   \textbf{hFacMin}\textit{\ } needs to be set to a value between 0 and
-(it is set to 1 by default) corresponding to the minimum
-   fractional size of the cell. For example if the bottom cell is 500m
-   thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the actual
-   thickness of the cell (i.e. used in the code) can cover a range of
-   discrete values 50m apart from 50m to 500m depending on the value of
-   the bottom depth (in \textbf{bathyFile}) at this point.
-   Note that the bottom depths (or pressures) need not coincide with
-   the models levels as deduced from \textbf{delz}\textit{\
-   }or\textit{\ }\textbf{delp} \textit{. }The model will interpolate
-   the numbers in \textbf{bathyFile} \textit{\ }so that they match the
-   levels obtained from \textbf{delz}\textit{ \ }or\textit{\
-   }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
-   (Note: the atmospheric case is a bit more complicated than what is
-   written here I think. To come soon...)
- \item[time-discretization] \
-   The time steps are set through the real variables \textbf{deltaTMom}
-   and \textbf{deltaTtracer} (in s) which represent the time step for
-   the momentum and tracer equations, respectively. For synchronous
-   integrations, simply set the two variables to the same value (or you
-   can prescribe one time step only through the variable
-   \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
-   through the variable \textbf{abEps} (dimensionless). The stagger
-   baroclinic time stepping can be activated by setting the logical
-   variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
- \end{description}
- \subsection{Equation of state}
- First, because the model equations are written in terms of
- perturbations, a reference thermodynamic state needs to be specified.
- This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}.
- \textbf{tRef} specifies the reference potential temperature profile
- (in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting
- from the level k=1. Similarly, \textbf{sRef} specifies the reference
- salinity profile (in ppt) for the ocean or the reference specific
- humidity profile (in g/kg) for the atmosphere.
- The form of the equation of state is controlled by the character
- variables \textbf{buoyancyRelation} and \textbf{eosType}.
- \textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and
- needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations.
- In this case, \textbf{eosType} must be set to '\texttt{IDEALGAS}'.
- For the ocean, two forms of the equation of state are available:
- linear (set \textbf{eosType} to '\texttt{LINEAR}') and a polynomial
- approximation to the full nonlinear equation ( set
- \textbf{eosType}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear
- case, you need to specify the thermal and haline expansion
- coefficients represented by the variables \textbf{tAlpha}\textit{\
-   }(in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For the nonlinear
- case, you need to generate a file of polynomial coefficients called
- \textit{POLY3.COEFFS}. To do this, use the program
- \textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is
- available in the same directory and you will need to edit the number
- and the values of the vertical levels in \textit{knudsen2.f} so that
- they match those of your configuration).
- There there are also higher polynomials for the equation of state:
- \begin{description}
- \item['\texttt{UNESCO}':] The UNESCO equation of state formula of
-   Fofonoff and Millard \cite{fofonoff83}. This equation of state
-   assumes in-situ temperature, which is not a model variable; \emph{its use
-   is therefore discouraged, and it is only listed for completeness}.
- \item['\texttt{JMD95Z}':] A modified UNESCO formula by Jackett and
-   McDougall \cite{jackett95}, which uses the model variable potential
-   temperature as input. The '\texttt{Z}' indicates that this equation
-   of state uses a horizontally and temporally constant pressure
-   $p_{0}=-g\rho_{0}z$.
- \item['\texttt{JMD95P}':] A modified UNESCO formula by Jackett and
-   McDougall \cite{jackett95}, which uses the model variable potential
-   temperature as input. The '\texttt{P}' indicates that this equation
-   of state uses the actual hydrostatic pressure of the last time
-   step. Lagging the pressure in this way requires an additional pickup
-   file for restarts.
- \item['\texttt{MDJWF}':] The new, more accurate and less expensive
-   equation of state by McDougall et~al. \cite{mcdougall03}. It also
-   requires lagging the pressure and therefore an additional pickup
-   file for restarts.
- \end{description}
- For none of these options an reference profile of temperature or
- salinity is required.
- \subsection{Momentum equations}
- In this section, we only focus for now on the parameters that you are likely
+ The MNC output files are all in the ``self-describing'' netCDF
- to change, i.e. the ones relative to forcing and dissipation for example.
+ format and can thus be browsed and/or plotted using tools such as:
- The details relevant to the vector-invariant form of the equations and the
+ \begin{itemize}
- various advection schemes are not covered for the moment. We assume that you
+ \item \texttt{ncdump} is a utility which is typically included
- use the standard form of the momentum equations (i.e. the flux-form) with
+   with every netCDF install:
- the default advection scheme. Also, there are a few logical variables that
+   \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
- allow you to turn on/off various terms in the momentum equation. These
+ \begin{verbatim}
- variables are called \textbf{momViscosity, momAdvection, momForcing,
+ http://www.unidata.ucar.edu/packages/netcdf/
- useCoriolis, momPressureForcing, momStepping}\textit{, }and \textit{\ }%
+ \end{verbatim}
- \textbf{metricTerms }and are assumed to be set to '.\texttt{TRUE}.' here.
+   \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
- Look at the file \textit{model/inc/PARAMS.h }for a precise definition of
+   binaries into formatted ASCII text files.
- these variables.
- \begin{description}
- \item[initialization] \
-   The velocity components are initialized to 0 unless the simulation
-   is starting from a pickup file (see section on simulation control
-   parameters).
- \item[forcing] \
-   This section only applies to the ocean. You need to generate
-   wind-stress data into two files \textbf{zonalWindFile}\textit{\ }and
-   \textbf{ meridWindFile }corresponding to the zonal and meridional
-   components of the wind stress, respectively (if you want the stress
-   to be along the direction of only one of the model horizontal axes,
-   you only need to generate one file). The format of the files is
-   similar to the bathymetry file. The zonal (meridional) stress data
-   are assumed to be in Pa and located at U-points (V-points). As for
-   the bathymetry, the precision with which to read the binary data is
-   controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } See
-   the matlab program \textit{gendata.m }in the \textit{input
-   }directories under \textit{verification }to see how simple
-   analytical wind forcing data are generated for the case study
-   experiments.
-   There is also the possibility of prescribing time-dependent periodic
-   forcing. To do this, concatenate the successive time records into a
-   single file (for each stress component) ordered in a (x, y, t)
-   fashion and set the following variables:
-   \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
-   \textbf{externForcingPeriod }to the period (in s) of which the
-   forcing varies (typically 1 month), and \textbf{externForcingCycle
-   }to the repeat time (in s) of the forcing (typically 1 year -- note:
-   \textbf{ externForcingCycle }must be a multiple of
-   \textbf{externForcingPeriod}).  With these variables set up, the
-   model will interpolate the forcing linearly at each iteration.
- \item[dissipation] \
-   The lateral eddy viscosity coefficient is specified through the
-   variable \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The
-   vertical eddy viscosity coefficient is specified through the
-   variable \textbf{viscAz }(in m$^{2}$s$ ^{-1}$) for the ocean and
-   \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) for the atmosphere.
-   The vertical diffusive fluxes can be computed implicitly by setting
-   the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}
-   .'. In addition, biharmonic mixing can be added as well through the
-   variable \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a
-   spherical polar grid, you might also need to set the variable
-   \textbf{cosPower} which is set to 0 by default and which represents
-   the power of cosine of latitude to multiply viscosity. Slip or
-   no-slip conditions at lateral and bottom boundaries are specified
-   through the logical variables \textbf{no\_slip\_sides}\textit{\ }
-   and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}',
-   free-slip boundary conditions are applied. If no-slip boundary
-   conditions are applied at the bottom, a bottom drag can be applied
-   as well. Two forms are available: linear (set the variable
-   \textbf{bottomDragLinear}\textit{\ }in s$ ^{-1}$) and quadratic (set
-   the variable \textbf{bottomDragQuadratic}\textit{ \ }in m$^{-1}$).
-   The Fourier and Shapiro filters are described elsewhere.
- \item[C-D scheme] \
-   If you run at a sufficiently coarse resolution, you will need the
-   C-D scheme for the computation of the Coriolis terms. The
-   variable\textbf{\ tauCD}, which represents the C-D scheme coupling
-   timescale (in s) needs to be set.
- \item[calculation of pressure/geopotential] \
-   First, to run a non-hydrostatic ocean simulation, set the logical
-   variable \textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure
-   field is then inverted through a 3D elliptic equation. (Note: this
-   capability is not available for the atmosphere yet.) By default, a
-   hydrostatic simulation is assumed and a 2D elliptic equation is used
-   to invert the pressure field. The parameters controlling the
-   behaviour of the elliptic solvers are the variables
-   \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual } for
-   the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{
-     cg3dTargetResidual }for the 3D case. You probably won't need to
-   alter the default values (are we sure of this?).
-   For the calculation of the surface pressure (for the ocean) or
-   surface geopotential (for the atmosphere) you need to set the
-   logical variables \textbf{rigidLid} and
-   \textbf{implicitFreeSurface}\textit{\ }(set one to '.
-   \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how
-   you want to deal with the ocean upper or atmosphere lower boundary).
- \end{description}
- \subsection{Tracer equations}
- This section covers the tracer equations i.e. the potential temperature
- equation and the salinity (for the ocean) or specific humidity (for the
- atmosphere) equation. As for the momentum equations, we only describe for
- now the parameters that you are likely to change. The logical variables
- \textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{
- tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off
- terms in the temperature equation (same thing for salinity or specific
- humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{
- saltAdvection}\textit{\ }etc). These variables are all assumed here to be
- set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a
- precise definition.
- \begin{description}
- \item[initialization] \
-   The initial tracer data can be contained in the binary files
-   \textbf{ hydrogThetaFile }and \textbf{hydrogSaltFile}. These files
-   should contain 3D data ordered in an (x, y, r) fashion with k=1 as
-   the first vertical level.  If no file names are provided, the
-   tracers are then initialized with the values of \textbf{tRef }and
-   \textbf{sRef }mentioned above (in the equation of state section). In
-   this case, the initial tracer data are uniform in x and y for each
-   depth level.
- \item[forcing] \
-   This part is more relevant for the ocean, the procedure for the
-   atmosphere not being completely stabilized at the moment.
-   A combination of fluxes data and relaxation terms can be used for
-   driving the tracer equations. \ For potential temperature, heat flux
-   data (in W/m$ ^{2}$) can be stored in the 2D binary file
-   \textbf{surfQfile}\textit{. }  Alternatively or in addition, the
-   forcing can be specified through a relaxation term. The SST data to
-   which the model surface temperatures are restored to are supposed to
-   be stored in the 2D binary file \textbf{ thetaClimFile}\textit{.
-   }The corresponding relaxation time scale coefficient is set through
-   the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The same
-   procedure applies for salinity with the variable names
-   \textbf{EmPmRfile }\textit{, }\textbf{saltClimFile}\textit{, }and
-   \textbf{tauSaltClimRelax} \textit{\ }for freshwater flux (in m/s)
-   and surface salinity (in ppt) data files and relaxation time scale
-   coefficient (in s), respectively. Also for salinity, if the CPP key
-   \textbf{USE\_NATURAL\_BCS} is turned on, natural boundary conditions
-   are applied i.e. when computing the surface salinity tendency, the
-   freshwater flux is multiplied by the model surface salinity instead
-   of a constant salinity value.
-   As for the other input files, the precision with which to read the
-   data is controlled by the variable \textbf{readBinaryPrec}.
-   Time-dependent, periodic forcing can be applied as well following
-   the same procedure used for the wind forcing data (see above).
- \item[dissipation] \
-   Lateral eddy diffusivities for temperature and salinity/specific
-   humidity are specified through the variables \textbf{diffKhT }and
-   \textbf{diffKhS } (in m$^{2}$/s). Vertical eddy diffusivities are
-   specified through the variables \textbf{diffKzT }and \textbf{diffKzS
-   }(in m$^{2}$/s) for the ocean and \textbf{diffKpT }and
-   \textbf{diffKpS }(in Pa$^{2}$/s) for the atmosphere. The vertical
-   diffusive fluxes can be computed implicitly by setting the logical
-   variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'. In
-   addition, biharmonic diffusivities can be specified as well through
-   the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in
-   m$^{4}$/s). Note that the cosine power scaling (specified through
-   \textbf{cosPower }- see the momentum equations section) is applied
-   to the tracer diffusivities (Laplacian and biharmonic) as well. The
-   Gent and McWilliams parameterization for oceanic tracers is
-   described in the package section. Finally, note that tracers can be
-   also subject to Fourier and Shapiro filtering (see the corresponding
-   section on these filters).
- \item[ocean convection] \
-   Two options are available to parameterize ocean convection: one is
-   to use the convective adjustment scheme. In this case, you need to
-   set the variable \textbf{cadjFreq}, which represents the frequency
-   (in s) with which the adjustment algorithm is called, to a non-zero
-   value (if set to a negative value by the user, the model will set it
-   to the tracer time step). The other option is to parameterize
-   convection with implicit vertical diffusion. To do this, set the
-   logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'
-   and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s)
-   you wish the tracer vertical diffusivities to have when mixing
-   tracers vertically due to static instabilities. Note that
-   \textbf{cadjFreq }and \textbf{ivdc\_kappa }can not both have
-   non-zero value.
- \end{description}
- \subsection{Simulation controls}
- The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s)
- which determines the IO frequencies and is used in tagging output.
- Typically, you will set it to the tracer time step for accelerated runs
- (otherwise it is simply set to the default time step \textbf{deltaT}).
- Frequency of checkpointing and dumping of the model state are referenced to
- this clock (see below).
- \begin{description}
+ \item \texttt{ncview} utility is a very convenient and quick way
- \item[run duration] \
+   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}
-   The beginning of a simulation is set by specifying a start time (in
+ \item MatLAB(c) and other common post-processing environments provide
-   s) through the real variable \textbf{startTime }or by specifying an
+   various netCDF interfaces including:
-   initial iteration number through the integer variable
+   \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
-   \textbf{nIter0}. If these variables are set to nonzero values, the
+ \begin{verbatim}
-   model will look for a ''pickup'' file \textit{pickup.0000nIter0 }to
+ http://mexcdf.sourceforge.net/
-   restart the integration\textit{. }The end of a simulation is set
+ \end{verbatim}
-   through the real variable \textbf{endTime }(in s).  Alternatively,
+   \begin{rawhtml} </A> \end{rawhtml}
-   you can specify instead the number of time steps to execute through
+   \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
-   the integer variable \textbf{nTimeSteps}.
+ \begin{verbatim}
+ http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
- \item[frequency of output] \
+ \end{verbatim}
+   \begin{rawhtml} </A> \end{rawhtml}
-   Real variables defining frequencies (in s) with which output files
+ \end{itemize}
-   are written on disk need to be set up. \textbf{dumpFreq }controls
-   the frequency with which the instantaneous state of the model is
-   saved. \textbf{chkPtFreq } and \textbf{pchkPtFreq }control the
-   output frequency of rolling and permanent checkpoint files,
-   respectively. See section 1.5.1 Output files for the definition of
-   model state and checkpoint files. In addition, time-averaged fields
-   can be written out by setting the variable \textbf{taveFreq} (in s).
-   The precision with which to write the binary data is controlled by
-   the integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32}
-   or \texttt{ 64}).
- \end{description}
- %%% Local Variables:
- %%% mode: latex
- %%% TeX-master: t
- %%% End:

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