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revision 1.24 by edhill, Fri Apr 9 15:06:18 2004 UTC revision 1.42 by jmc, Fri May 28 02:09:59 2010 UTC
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3    
4  %\section{Getting started}  %\section{Getting started}
5    
6  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  
7  model is to run the case study examples provided with the base  model is to run the case study examples provided with the base
8  version. Information on how to obtain, compile, and run the code is  version. Information on how to obtain, compile, and run the code is
9  found there as well as a brief description of the model structure  found here as well as a brief description of the model structure
10  directory and the case study examples.  The latter and the code  directory and the case study examples. Information is also provided
11  structure are described more fully in chapters  here on how to customize the code when you are ready to try implementing
12  \ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in  the configuration you have in mind.  The code and algorithm
13  this section, we provide information on how to customize the code when  are described more fully in chapters \ref{chap:discretization} and
14  you are ready to try implementing the configuration you have in mind.  \ref{chap:sarch}.
15    
16  \section{Where to find information}  \section{Where to find information}
17  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
18    \begin{rawhtml}
19    <!-- CMIREDIR:whereToFindInfo: -->
20    \end{rawhtml}
21    
22  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  
23  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
24  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
25  \begin{verbatim}  \begin{verbatim}
# Line 37  http://mitgcm.org/mailman/listinfo/mitgc Line 27  http://mitgcm.org/mailman/listinfo/mitgc
27  http://mitgcm.org/pipermail/mitgcm-support/  http://mitgcm.org/pipermail/mitgcm-support/
28  \end{verbatim}  \end{verbatim}
29  \begin{rawhtml} </A> \end{rawhtml}  \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  
   
   
30    
31  \section{Obtaining the code}  \section{Obtaining the code}
32  \label{sect:obtainingCode}  \label{sect:obtainingCode}
33    \begin{rawhtml}
34    <!-- CMIREDIR:obtainingCode: -->
35    \end{rawhtml}
36    
37  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
38  the instructions below. As a courtesy we ask that you send e-mail to us at  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
62    
63  \end{enumerate}  \end{enumerate}
64    
65  \subsubsection{Checkout from CVS}  \subsection{Method 1 - Checkout from CVS}
66  \label{sect:cvs_checkout}  \label{sect:cvs_checkout}
67    
68  If CVS is available on your system, we strongly encourage you to use it. CVS  If CVS is available on your system, we strongly encourage you to use it. CVS
# Line 92  be set within your shell.  For a csh or Line 75  be set within your shell.  For a csh or
75  \begin{verbatim}  \begin{verbatim}
76  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
77  \end{verbatim}  \end{verbatim}
78  in your .cshrc or .tcshrc file.  For bash or sh shells, put:  in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
79    shells, put:
80  \begin{verbatim}  \begin{verbatim}
81  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
82  \end{verbatim}  \end{verbatim}
# Line 118  The MITgcm web site contains further dir Line 102  The MITgcm web site contains further dir
102  code and CVS.  It also contains a web interface to our CVS archive so  code and CVS.  It also contains a web interface to our CVS archive so
103  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
104  development milestones:  development milestones:
105  \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}  %\begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
106    \begin{rawhtml} <A href="http://mitgcm.org/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
107  \begin{verbatim}  \begin{verbatim}
108  http://mitgcm.org/source_code.html  http://mitgcm.org/source_code.html
109  \end{verbatim}  \end{verbatim}
# Line 147  of CVS aliases Line 132  of CVS aliases
132    \label{tab:cvsModules}    \label{tab:cvsModules}
133  \end{table}  \end{table}
134    
135  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \texttt{MITgcm}. If
136  the directory \textit{MITgcm} exists this command updates your code  the directory \texttt{MITgcm} exists this command updates your code
137  based on the repository. Each directory in the source tree contains a  based on the repository. Each directory in the source tree contains a
138  directory \textit{CVS}. This information is required by CVS to keep  directory \texttt{CVS}. This information is required by CVS to keep
139  track of your file versions with respect to the repository. Don't edit  track of your file versions with respect to the repository. Don't edit
140  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
141  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
142  MITgcm code can be found  MITgcm code can be found
143  \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}
144  here  here
145  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
146  .  .
# Line 168  they create can be changed to a differen Line 153  they create can be changed to a differen
153     %  mv MITgcm MITgcm_verif_basic     %  mv MITgcm MITgcm_verif_basic
154  \end{verbatim}  \end{verbatim}
155    
   
 \subsubsection{Conventional download method}  
 \label{sect:conventionalDownload}  
   
 If you do not have CVS on your system, you can download the model as a  
 tar file from the web site at:  
 \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/download/  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 The tar file still contains CVS information which we urge you not to  
 delete; even if you do not use CVS yourself the information can help  
 us if you should need to send us your copy of the code.  If a recent  
 tar file does not exist, then please contact the developers through  
 the  
 \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  
 MITgcm-support@mitgcm.org  
 \begin{rawhtml} </A> \end{rawhtml}  
 mailing list.  
   
156  \subsubsection{Upgrading from an earlier version}  \subsubsection{Upgrading from an earlier version}
157    
158  If you already have an earlier version of the code you can ``upgrade''  If you already have an earlier version of the code you can ``upgrade''
# Line 255  that you may only have part of a patch. Line 219  that you may only have part of a patch.
219  also means we can't tell what version of the code you are working  also means we can't tell what version of the code you are working
220  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
221    
222    \subsection{Method 2 - Tar file download}
223    \label{sect:conventionalDownload}
224    
225    If you do not have CVS on your system, you can download the model as a
226    tar file from the web site at:
227    \begin{rawhtml} <A href=http://mitgcm.org/download/ target="idontexist"> \end{rawhtml}
228    \begin{verbatim}
229    http://mitgcm.org/download/
230    \end{verbatim}
231    \begin{rawhtml} </A> \end{rawhtml}
232    The tar file still contains CVS information which we urge you not to
233    delete; even if you do not use CVS yourself the information can help
234    us if you should need to send us your copy of the code.  If a recent
235    tar file does not exist, then please contact the developers through
236    the
237    \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
238    MITgcm-support@mitgcm.org
239    \begin{rawhtml} </A> \end{rawhtml}
240    mailing list.
241    
242  \section{Model and directory structure}  \section{Model and directory structure}
243    \begin{rawhtml}
244    <!-- CMIREDIR:directory_structure: -->
245    \end{rawhtml}
246    
247  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
248  support wrapper. This wrapper is designed to provide a general  support wrapper. This wrapper is designed to provide a general
# Line 263  framework for grid-point models. MITgcmU Line 250  framework for grid-point models. MITgcmU
250  model that uses the framework. Under this structure the model is split  model that uses the framework. Under this structure the model is split
251  into execution environment support code and conventional numerical  into execution environment support code and conventional numerical
252  model code. The execution environment support code is held under the  model code. The execution environment support code is held under the
253  \textit{eesupp} directory. The grid point model code is held under the  \texttt{eesupp} directory. The grid point model code is held under the
254  \textit{model} directory. Code execution actually starts in the  \texttt{model} directory. Code execution actually starts in the
255  \textit{eesupp} routines and not in the \textit{model} routines. For  \texttt{eesupp} routines and not in the \texttt{model} routines. For
256  this reason the top-level \textit{MAIN.F} is in the  this reason the top-level \texttt{MAIN.F} is in the
257  \textit{eesupp/src} directory. In general, end-users should not need  \texttt{eesupp/src} directory. In general, end-users should not need
258  to worry about this level. The top-level routine for the numerical  to worry about this level. The top-level routine for the numerical
259  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
260  a brief description of the directory structure of the model under the  a brief description of the directory structure of the model under the
261  root tree (a detailed description is given in section 3: Code  root tree (a detailed description is given in section 3: Code
262  structure).  structure).
263    
264  \begin{itemize}  \begin{itemize}
265    
266  \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.  
267        
268  \item \textit{eesupp}: contains the execution environment source code.  \item \texttt{eesupp}: contains the execution environment source code.
269    Also subdivided into two subdirectories \textit{inc} and    Also subdivided into two subdirectories \texttt{inc} and
270    \textit{src}.    \texttt{src}.
271      
272    \item \texttt{model}: this directory contains the main source code.
273      Also subdivided into two subdirectories \texttt{inc} and
274      \texttt{src}.
275        
276  \item \textit{exe}: this directory is initially empty. It is the  \item \texttt{pkg}: contains the source code for the packages. Each
277    default directory in which to execute the code.    package corresponds to a subdirectory. For example, \texttt{gmredi}
     
 \item \textit{model}: this directory contains the main source code.  
   Also subdivided into two subdirectories \textit{inc} and  
   \textit{src}.  
     
 \item \textit{pkg}: contains the source code for the packages. Each  
   package corresponds to a subdirectory. For example, \textit{gmredi}  
278    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
279    \textit{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
280    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in chapter \ref{chap.packagesI}.
281        
282  \item \textit{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
283    For example, \textit{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
284    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
285    \textit{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
286    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
287    The latter is described in details in part V.    The latter is described in detail in part \ref{chap.ecco}.
288      This directory also contains the subdirectory build\_options, which
289      contains the `optfiles' with the compiler options for the different
290      compilers and machines that can run MITgcm.
291        
292  \item \textit{utils}: this directory contains various utilities. The  \item \texttt{utils}: this directory contains various utilities. The
293    subdirectory \textit{knudsen2} contains code and a makefile that    subdirectory \texttt{knudsen2} contains code and a makefile that
294    compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
295    formula for an ocean nonlinear equation of state. The    formula for an ocean nonlinear equation of state. The
296    \textit{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
297    model output directly into matlab. \textit{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
298    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
299    model output.    model output. The subdirectory exch2 contains the code needed for
300      the exch2 package to work with different combinations of domain
301      decompositions.
302        
303  \item \textit{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
304    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sect:modelExamples}.
305    
306  \end{itemize}  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
   
 \section{Example experiments}  
 \label{sect:modelExamples}  
   
 %% a set of twenty-four pre-configured numerical experiments  
   
 The MITgcm distribution comes with more than a dozen pre-configured  
 numerical experiments. Some of these example experiments are tests of  
 individual parts of the model code, but many are fully fledged  
 numerical simulations. A few of the examples are used for tutorial  
 documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.  
 The other examples follow the same general structure as the tutorial  
 examples. However, they only include brief instructions in a text file  
 called {\it README}.  The examples are located in subdirectories under  
 the directory \textit{verification}. Each example is briefly described  
 below.  
   
 \subsection{Full list of model examples}  
   
 \begin{enumerate}  
     
 \item \textit{exp0} - single layer, ocean double gyre (barotropic with  
   free-surface). This experiment is described in detail in section  
   \ref{sect:eg-baro}.  
   
 \item \textit{exp1} - Four layer, ocean double gyre. This experiment  
   is described in detail in section \ref{sect:eg-baroc}.  
     
 \item \textit{exp2} - 4x4 degree global ocean simulation with steady  
   climatological forcing. This experiment is described in detail in  
   section \ref{sect:eg-global}.  
     
 \item \textit{exp4} - Flow over a Gaussian bump in open-water or  
   channel with open boundaries.  
     
 \item \textit{exp5} - Inhomogenously forced ocean convection in a  
   doubly periodic box.  
   
 \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for  
 Gent/McWilliams scheme). 2D (Y-Z).  
   
 \item \textit{internal wave} - Ocean internal wave forced by open  
   boundary conditions.  
     
 \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  
   scheme; 1 month integration  
     
 \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and  
   Suarez '94 forcing.  
     
 \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing.  
     
 \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing on the cubed sphere.  
     
 \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  
   Global Zonal Mean configuration, 1x64x5 resolution.  
     
 \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate  
   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).  
     
 \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  
   physics. 3D Equatorial Channel configuration.  
     
 \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.  
   Global configuration, on latitude longitude grid with 128x64x5 grid  
   points ($2.8^\circ{\rm degree}$ resolution).  
     
 \item \textit{adjustment.128x64x1} Barotropic adjustment problem on  
   latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on  
   cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \textit{advect\_cs} Two-dimensional passive advection test on  
   cube sphere grid.  
307        
308  \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive  \item \texttt{lsopt}: Line search code used for optimization.
   advection test on Cartesian grid.  
309        
310  \item \textit{advect\_yz} Two-dimensional (vertical plane) passive  \item \texttt{optim}: Interface between MITgcm and line search code.
   advection test on Cartesian grid.  
311        
 \item \textit{carbon} Simple passive tracer experiment. Includes  
   derivative calculation. Described in detail in section  
   \ref{sect:eg-carbon-ad}.  
   
 \item \textit{flt\_example} Example of using float package.  
     
 \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux  
   boundary conditions and poles.  
   
 \item \textit{global\_ocean\_pressure} Global circulation in pressure  
   coordinate (non-Boussinesq ocean model). Described in detail in  
   section \ref{sect:eg-globalpressure}.  
     
 \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube  
   sphere grid.  
   
 \end{enumerate}  
   
 \subsection{Directory structure of model examples}  
   
 Each example directory has the following subdirectories:  
   
 \begin{itemize}  
 \item \textit{code}: contains the code particular to the example. At a  
   minimum, this directory includes the following files:  
   
   \begin{itemize}  
   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to  
     the ``execution environment'' part of the code. The default  
     version is located in \textit{eesupp/inc}.  
     
   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to  
     the ``numerical model'' part of the code. The default version is  
     located in \textit{model/inc}.  
     
   \item \textit{code/SIZE.h}: declares size of underlying  
     computational grid.  The default version is located in  
     \textit{model/inc}.  
   \end{itemize}  
     
   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  
     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.  
312  \end{itemize}  \end{itemize}
313    
314  Once you have chosen the example you want to run, you are ready to  \section[Building MITgcm]{Building the code}
 compile the code.  
   
 \section{Building the code}  
315  \label{sect:buildingCode}  \label{sect:buildingCode}
316    \begin{rawhtml}
317  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
318  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
319  compiler and optimization options and also figures out any file  
320  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
321  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
322    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
323    file dependencies. We supply a script (\texttt{genmake2}), described
324    in section \ref{sect:genmake}, that automatically creates the
325    \texttt{Makefile} for you. You then need to build the dependencies and
326  compile the code.  compile the code.
327    
328  As an example, let's assume that you want to build and run experiment  As an example, assume that you want to build and run experiment
329  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
330  actually do this but here let's build the code in  actually do this but here let's build the code in
331  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
332  \begin{verbatim}  \begin{verbatim}
333  % cd verification/exp2/input  % cd verification/exp2/build
334  \end{verbatim}  \end{verbatim}
335  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
336  \begin{verbatim}  \begin{verbatim}
337  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
338  \end{verbatim}  \end{verbatim}
339  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
340  code with any files in the directory {\em ./code/}.  code with any files in the directory \texttt{../code/}.
341    
342  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
343  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
344  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
345  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
346    tools/build\_options} directory.  Under some circumstances, a user  the \texttt{tools/build\_options} directory.  Under some
347  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
348  combination of compiler, compiler flags, libraries, and other options  specify the exact combination of compiler, compiler flags, libraries,
349  necessary to build a particular configuration of MITgcm.  In such  and other options necessary to build a particular configuration of
350  cases, it is generally helpful to read the existing ``optfiles'' and  MITgcm.  In such cases, it is generally helpful to read the existing
351  mimic their syntax.  ``optfiles'' and mimic their syntax.
352    
353  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
354  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
355  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
356  architectures) to the  architectures) to the
357  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
358  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
359  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
360  list.  list.
361    
362  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
363  \begin{verbatim}  \begin{verbatim}
364  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
365  \end{verbatim}  \end{verbatim}
366    
367  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
368    dependencies with the command:
369  \begin{verbatim}  \begin{verbatim}
370  % make depend  % make depend
371  \end{verbatim}  \end{verbatim}
372  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
373  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
374  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
375    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
376  directory.  this directory.  It is important to note that the {\tt make depend}
377    stage will occasionally produce warnings or errors since the
378    dependency parsing tool is unable to find all of the necessary header
379    files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
380    is usually OK to ignore the warnings/errors and proceed to the next
381    step.
382    
383  Next compile the code:  Next one can compile the code using:
384  \begin{verbatim}  \begin{verbatim}
385  % make  % make
386  \end{verbatim}  \end{verbatim}
387  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
388  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
389  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
390    (shared multi-processor) systems, the build process can often be sped
391    up appreciably using the command:
392    \begin{verbatim}
393    % make -j 2
394    \end{verbatim}
395    where the ``2'' can be replaced with a number that corresponds to the
396    number of CPUs available.
397    
398  Now you are ready to run the model. General instructions for doing so are  Now you are ready to run the model. General instructions for doing so are
399  given in section \ref{sect:runModel}. Here, we can run the model with:  given in section \ref{sect:runModel}. Here, we can run the model by
400    first creating links to all the input files:
401    \begin{verbatim}
402    ln -s ../input/* .
403    \end{verbatim}
404    and then calling the executable with:
405  \begin{verbatim}  \begin{verbatim}
406  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
407  \end{verbatim}  \end{verbatim}
408  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
409  output.txt}.  \texttt{output.txt}.
   
410    
411  \subsection{Building/compiling the code elsewhere}  \subsection{Building/compiling the code elsewhere}
412    
# Line 673  To compile the code, first use the progr Line 520  To compile the code, first use the progr
520  in the \texttt{tools} directory) to generate a Makefile.  in the \texttt{tools} directory) to generate a Makefile.
521  \texttt{genmake2} is a shell script written to work with all  \texttt{genmake2} is a shell script written to work with all
522  ``sh''--compatible shells including bash v1, bash v2, and Bourne.  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
523  Internally, \texttt{genmake2} determines the locations of needed  %Internally, \texttt{genmake2} determines the locations of needed
524  files, the compiler, compiler options, libraries, and Unix tools.  It  %files, the compiler, compiler options, libraries, and Unix tools.  It
525  relies upon a number of ``optfiles'' located in the  %relies upon a number of ``optfiles'' located in the
526  \texttt{tools/build\_options} directory.  %\texttt{tools/build\_options} directory.
527    \texttt{genmake2} parses information from the following sources:
528    \begin{description}
529    \item[-] a {\em gemake\_local} file if one is found in the current
530      directory
531    \item[-] command-line options
532    \item[-] an "options file" as specified by the command-line option
533      \texttt{--optfile=/PATH/FILENAME}
534    \item[-] a {\em packages.conf} file (if one is found) with the
535      specific list of packages to compile. The search path for
536      file {\em packages.conf} is, first, the current directory and
537      then each of the "MODS" directories in the given order (see below).
538    \end{description}
539    
540    \subsubsection{Optfiles in \texttt{tools/build\_options} directory:}
541    
542  The purpose of the optfiles is to provide all the compilation options  The purpose of the optfiles is to provide all the compilation options
543  for particular ``platforms'' (where ``platform'' roughly means the  for particular ``platforms'' (where ``platform'' roughly means the
# Line 749  for inclusion.  Please send the file to Line 610  for inclusion.  Please send the file to
610  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
611  mailing list.  mailing list.
612    
613    \subsubsection{Command-line options:}
614    
615  In addition to the optfiles, \texttt{genmake2} supports a number of  In addition to the optfiles, \texttt{genmake2} supports a number of
616  helpful command-line options.  A complete list of these options can be  helpful command-line options.  A complete list of these options can be
617  obtained from:  obtained from:
# Line 771  The most important command-line options Line 634  The most important command-line options
634    the user's path.  When these three items have been identified,    the user's path.  When these three items have been identified,
635    genmake2 will try to find an optfile that has a matching name.    genmake2 will try to find an optfile that has a matching name.
636        
637  \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default  \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
638    set of packages to be used.  The normal order of precedence for    directories containing ``modifications''.  These directories contain
639    packages is as follows:    files with names that may (or may not) exist in the main MITgcm
640    \begin{enumerate}    source tree but will be overridden by any identically-named sources
641    \item If available, the command line (\texttt{--pdefault}) settings    within the ``MODS'' directories.
642      over-rule any others.    
643      The order of precedence for this "name-hiding" is as follows:
644    \item Next, \texttt{genmake2} will look for a file named    \begin{itemize}
645      ``\texttt{packages.conf}'' in the local directory or in any of the    \item ``MODS'' directories (in the order given)
646      directories specified with the \texttt{--mods} option.    \item Packages either explicitly specified or provided by default
647            (in the order given)
648    \item Finally, if neither of the above are available,    \item Packages included due to package dependencies (in the order
649      \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.      that that package dependencies are parsed)
650    \end{enumerate}    \item The "standard dirs" (which may have been specified by the
651        ``-standarddirs'' option)
652      \end{itemize}
653        
654    \item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
655      where package groups are defined. If not set, the package-groups
656      definition will be read from {\em pkg/pkg\_groups}.
657      It also contains the default list of packages (defined
658      as the group ``{\it default\_pkg\_list}'' which is used
659      when no specific package list ({\em packages.conf})
660      is found in current directory or in any "MODS" directory.
661    
662  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
663    used for packages.    used for packages.
664        
# Line 810  The most important command-line options Line 683  The most important command-line options
683    "STAF" compiler.  As with any compilers, it is helpful to have their    "STAF" compiler.  As with any compilers, it is helpful to have their
684    directories listed in your {\tt \$PATH} environment variable.    directories listed in your {\tt \$PATH} environment variable.
685        
 \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}  
     
686  \item[\texttt{--mpi}] This option enables certain MPI features (using  \item[\texttt{--mpi}] This option enables certain MPI features (using
687    CPP \texttt{\#define}s) within the code and is necessary for MPI    CPP \texttt{\#define}s) within the code and is necessary for MPI
688    builds (see Section \ref{sect:mpi-build}).    builds (see Section \ref{sect:mpi-build}).
# Line 869  The steps for building MITgcm with MPI s Line 725  The steps for building MITgcm with MPI s
725    libraries and put them into an options file as described in Section    libraries and put them into an options file as described in Section
726    \ref{sect:genmake}.  One can start with one of the examples in:    \ref{sect:genmake}.  One can start with one of the examples in:
727    \begin{rawhtml} <A    \begin{rawhtml} <A
728      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
729    \end{rawhtml}    \end{rawhtml}
730    \begin{center}    \begin{center}
731      \texttt{MITgcm/tools/build\_options/}      \texttt{MITgcm/tools/build\_options/}
# Line 920  The steps for building MITgcm with MPI s Line 776  The steps for building MITgcm with MPI s
776    library and a job scheduling and queueing system such as PBS,    library and a job scheduling and queueing system such as PBS,
777    LoadLeveller, Condor, or any of a number of similar tools.  A few    LoadLeveller, Condor, or any of a number of similar tools.  A few
778    example scripts (those used for our \begin{rawhtml} <A    example scripts (those used for our \begin{rawhtml} <A
779      href="http://mitgcm.org/testing.html"> \end{rawhtml}regular      href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
780    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
781    at:    at:
782    \begin{rawhtml} <A    \begin{rawhtml} <A
783      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/">
784    \end{rawhtml}    \end{rawhtml}
785    {\footnotesize \tt    {\footnotesize \tt
786      http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }      http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
787      \begin{rawhtml} </A> \end{rawhtml}
788      or at:
789      \begin{rawhtml} <A
790        href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
791      \end{rawhtml}
792      {\footnotesize \tt
793        http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
794    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
795    
796  \end{enumerate}  \end{enumerate}
797    
798    An example of the above process on the MITgcm cluster (``cg01'') using
799    the GNU g77 compiler and the mpich MPI library is:
800    
801    {\footnotesize \begin{verbatim}
802      %  cd MITgcm/verification/exp5
803      %  mkdir build
804      %  cd build
805      %  ../../../tools/genmake2 -mpi -mods=../code \
806           -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
807      %  make depend
808      %  make
809      %  cd ../input
810      %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
811           -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
812    \end{verbatim} }
813    
814  \section{Running the model}  \section[Running MITgcm]{Running the model in prognostic mode}
815  \label{sect:runModel}  \label{sect:runModel}
816    \begin{rawhtml}
817    <!-- CMIREDIR:runModel: -->
818    \end{rawhtml}
819    
820  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sect:buildingCode})
821  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
822  local directory.  local directory.
823    
824  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)
825  type:  simply type:
826  \begin{verbatim}  \begin{verbatim}
827  % ./mitgcmuv  % ./mitgcmuv
828  \end{verbatim}  \end{verbatim}
# Line 952  do!). The above command will spew out ma Line 832  do!). The above command will spew out ma
832  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
833  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
834  etc. It is worth keeping this text output with the binary output so we  etc. It is worth keeping this text output with the binary output so we
835  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
836  \begin{verbatim}  \begin{verbatim}
837  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
838  \end{verbatim}  \end{verbatim}
839    In the event that the model encounters an error and stops, it is very
840  For the example experiments in {\em verification}, an example of the  helpful to include the last few line of this \texttt{output.txt} file
841  output is kept in {\em results/output.txt} for comparison. You can compare  along with the (\texttt{stderr}) error message within any bug reports.
842  your {\em output.txt} with this one to check that the set-up works.  
843    For the example experiments in \texttt{verification}, an example of the
844    output is kept in \texttt{results/output.txt} for comparison. You can
845    compare your \texttt{output.txt} with the corresponding one for that
846    experiment to check that the set-up works.
847    
848    
849    
850  \subsection{Output files}  \subsection{Output files}
851    
852  The model produces various output files. At a minimum, the instantaneous  The model produces various output files and, when using \texttt{mnc},
853  ``state'' of the model is written out, which is made of the following files:  sometimes even directories.  Depending upon the I/O package(s)
854    selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
855    both as determined by \texttt{code/packages.conf}) and the run-time
856    flags set (in \texttt{input/data.pkg}), the following output may
857    appear.
858    
859    
860    \subsubsection{MDSIO output files}
861    
862    The ``traditional'' output files are generated by the \texttt{mdsio}
863    package.  At a minimum, the instantaneous ``state'' of the model is
864    written out, which is made of the following files:
865    
866  \begin{itemize}  \begin{itemize}
867  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
868  0 $ eastward).    and positive eastward).
869    
870  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
871  and $> 0$ northward).    (m/s and positive northward).
872    
873  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
874  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
875  i.e. downward).    towards increasing pressure i.e. downward).
876    
877  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
878  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
879    
880  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
881  (g/kg).    vapor (g/kg).
882    
883  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
884  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
885  \end{itemize}  \end{itemize}
886    
887  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
888  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
889  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
890    
891  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
892    
893  \begin{itemize}  \begin{itemize}
894  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
895  \end{itemize}  \end{itemize}
896    
897  is written out. This file represents the state of the model in a condensed  is written out. This file represents the state of the model in a condensed
# Line 1004  form and is used for restarting the inte Line 899  form and is used for restarting the inte
899  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
900    
901  \begin{itemize}  \begin{itemize}
902  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
903  \end{itemize}  \end{itemize}
904    
905  containing the D-grid velocity data and that has to be written out as well  containing the D-grid velocity data and that has to be written out as well
906  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
907  as the pickup files but are named differently. Their name contain the chain  as the pickup files but are named differently. Their name contain the chain
908  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
909  used to restart the model but are overwritten every other time they are  used to restart the model but are overwritten every other time they are
910  output to save disk space during long integrations.  output to save disk space during long integrations.
911    
912    \subsubsection{MNC output files}
913    
914    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
915    is usually (though not necessarily) placed within a subdirectory with
916    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  
917    
918  \subsection{Looking at the output}  \subsection{Looking at the output}
919    
920  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
921  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
922  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \texttt{.data} and \texttt{.meta}. The
923  binary form (big\_endian by default). The \textit{.meta} file is a  \texttt{.data} file contains the data written in binary form
924  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
925  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
926  particularly useful when running multi-processors calculations. The base  \texttt{.data} file. This way of organizing the output is particularly
927  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
928  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
929  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
930  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}
931    reads the data. Look at the comments inside the script to see how to
932    use it.
933    
934  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
935  \begin{verbatim}  \begin{verbatim}
# Line 1043  Some examples of reading and visualizing Line 946  Some examples of reading and visualizing
946  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
947  \end{verbatim}  \end{verbatim}
948    
949  \section{Doing it yourself: customizing the code}  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
950    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, and r directions are represented  
   by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr}  
   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 the section on  
   parallel implementation.)  
   
 \item[grid] \  
     
   Three different grids are available: cartesian, spherical polar, and  
   curvilinear (which includes the cubed sphere). The grid is set  
   through the logical variables \textbf{usingCartesianGrid},  
   \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}.  
   In the case of spherical and curvilinear grids, the southern  
   boundary is defined through the variable \textbf{phiMin} 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} and \textbf{dely} (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} 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 puts 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} and \textbf{beta} 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 } is set to a nonzero value, \textbf{f0} 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}. 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}  
   needs to be set to a value between 0 and 1 (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} 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} or \textbf{delp}.  
   The model will interpolate the numbers in \textbf{bathyFile} so that  
   they match the levels obtained from \textbf{delz} or \textbf{delp}  
   and \textbf{hFacMin}.  
     
   (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} to  
 \texttt{'POLYNOMIAL'}). In the linear case, you need to specify the  
 thermal and haline expansion coefficients represented by the variables  
 \textbf{tAlpha} (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; {\em 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 to change, i.e. the ones relative to forcing and dissipation  
 for example.  The details relevant to the vector-invariant form of the  
 equations and the various advection schemes are not covered for the  
 moment. We assume that you use the standard form of the momentum  
 equations (i.e. the flux-form) with the default advection scheme.  
 Also, there are a few logical variables that allow you to turn on/off  
 various terms in the momentum equation. These variables are called  
 \textbf{momViscosity, momAdvection, momForcing, useCoriolis,  
   momPressureForcing, momStepping} and \textbf{metricTerms }and are  
 assumed to be set to \texttt{'.TRUE.'} here.  Look at the file  
 \textit{model/inc/PARAMS.h }for a precise definition of 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} 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}.  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} (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} (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} (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} 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} in s$ ^{-1}$) and  
   quadratic (set the variable \textbf{bottomDragQuadratic} in  
   m$^{-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} and \textbf{cg2dTargetResidual } for  
   the 2D case and \textbf{cg3dMaxIters} 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}  
   (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} \textbf{tempAdvection}  
 \textbf{tempForcing}, 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},  
 \textbf{saltAdvection} 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}.  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}. The corresponding  
   relaxation time scale coefficient is set through the variable  
   \textbf{tauThetaClimRelax} (in s). The same procedure applies for  
   salinity with the variable names \textbf{EmPmRfile},  
   \textbf{saltClimFile}, and \textbf{tauSaltClimRelax} 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}  
951    
952  The model ''clock'' is defined by the variable \textbf{deltaTClock}  The MNC output files are all in the ``self-describing'' netCDF
953  (in s) which determines the IO frequencies and is used in tagging  format and can thus be browsed and/or plotted using tools such as:
954  output.  Typically, you will set it to the tracer time step for  \begin{itemize}
955  accelerated runs (otherwise it is simply set to the default time step  \item \texttt{ncdump} is a utility which is typically included
956  \textbf{deltaT}).  Frequency of checkpointing and dumping of the model    with every netCDF install:
957  state are referenced to this clock (see below).    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
958    \begin{verbatim}
959    http://www.unidata.ucar.edu/packages/netcdf/
960    \end{verbatim}
961      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
962      binaries into formatted ASCII text files.
963    
964  \begin{description}  \item \texttt{ncview} utility is a very convenient and quick way
965  \item[run duration] \    to plot netCDF data and it runs on most OSes:
966      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
967    \begin{verbatim}
968    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
969    \end{verbatim}
970      \begin{rawhtml} </A> \end{rawhtml}
971        
972    The beginning of a simulation is set by specifying a start time (in  \item MatLAB(c) and other common post-processing environments provide
973    s) through the real variable \textbf{startTime} or by specifying an    various netCDF interfaces including:
974    initial iteration number through the integer variable    \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
975    \textbf{nIter0}. If these variables are set to nonzero values, the  \begin{verbatim}
976    model will look for a ''pickup'' file \textit{pickup.0000nIter0} to  http://mexcdf.sourceforge.net/
977    restart the integration. The end of a simulation is set through the  \end{verbatim}
978    real variable \textbf{endTime} (in s).  Alternatively, you can    \begin{rawhtml} </A> \end{rawhtml}
979    specify instead the number of time steps to execute through the    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
980    integer variable \textbf{nTimeSteps}.  \begin{verbatim}
981    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
982  \item[frequency of output] \  \end{verbatim}
983        \begin{rawhtml} </A> \end{rawhtml}
984    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}  
   
985    
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