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revision 1.21 by edhill, Thu Mar 11 16:11:56 2004 UTC revision 1.43 by jmc, Fri May 28 21:04:18 2010 UTC
# Line 3  Line 3 
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/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
106  \begin{verbatim}  \begin{verbatim}
107  http://mitgcm.org/source_code.html  http://mitgcm.org/viewvc/MITgcm/MITgcm/
108  \end{verbatim}  \end{verbatim}
109  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
110    
# Line 147  of CVS aliases Line 131  of CVS aliases
131    \label{tab:cvsModules}    \label{tab:cvsModules}
132  \end{table}  \end{table}
133    
134  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \texttt{MITgcm}. If
135  the directory \textit{MITgcm} exists this command updates your code  the directory \texttt{MITgcm} exists this command updates your code
136  based on the repository. Each directory in the source tree contains a  based on the repository. Each directory in the source tree contains a
137  directory \textit{CVS}. This information is required by CVS to keep  directory \texttt{CVS}. This information is required by CVS to keep
138  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
139  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
140  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
141  MITgcm code can be found  MITgcm code can be found
142  \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}
143  here  here
144  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
145  .  .
# Line 168  they create can be changed to a differen Line 152  they create can be changed to a differen
152     %  mv MITgcm MITgcm_verif_basic     %  mv MITgcm MITgcm_verif_basic
153  \end{verbatim}  \end{verbatim}
154    
   
 \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.  
   
155  \subsubsection{Upgrading from an earlier version}  \subsubsection{Upgrading from an earlier version}
156    
157  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 218  that you may only have part of a patch.
218  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
219  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
220    
221    \subsection{Method 2 - Tar file download}
222    \label{sect:conventionalDownload}
223    
224    If you do not have CVS on your system, you can download the model as a
225    tar file from the web site at:
226    \begin{rawhtml} <A href=http://mitgcm.org/download/ target="idontexist"> \end{rawhtml}
227    \begin{verbatim}
228    http://mitgcm.org/download/
229    \end{verbatim}
230    \begin{rawhtml} </A> \end{rawhtml}
231    The tar file still contains CVS information which we urge you not to
232    delete; even if you do not use CVS yourself the information can help
233    us if you should need to send us your copy of the code.  If a recent
234    tar file does not exist, then please contact the developers through
235    the
236    \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
237    MITgcm-support@mitgcm.org
238    \begin{rawhtml} </A> \end{rawhtml}
239    mailing list.
240    
241  \section{Model and directory structure}  \section{Model and directory structure}
242    \begin{rawhtml}
243    <!-- CMIREDIR:directory_structure: -->
244    \end{rawhtml}
245    
246  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
247  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 249  framework for grid-point models. MITgcmU
249  model that uses the framework. Under this structure the model is split  model that uses the framework. Under this structure the model is split
250  into execution environment support code and conventional numerical  into execution environment support code and conventional numerical
251  model code. The execution environment support code is held under the  model code. The execution environment support code is held under the
252  \textit{eesupp} directory. The grid point model code is held under the  \texttt{eesupp} directory. The grid point model code is held under the
253  \textit{model} directory. Code execution actually starts in the  \texttt{model} directory. Code execution actually starts in the
254  \textit{eesupp} routines and not in the \textit{model} routines. For  \texttt{eesupp} routines and not in the \texttt{model} routines. For
255  this reason the top-level \textit{MAIN.F} is in the  this reason the top-level \texttt{MAIN.F} is in the
256  \textit{eesupp/src} directory. In general, end-users should not need  \texttt{eesupp/src} directory. In general, end-users should not need
257  to worry about this level. The top-level routine for the numerical  to worry about this level. The top-level routine for the numerical
258  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
259  a brief description of the directory structure of the model under the  a brief description of the directory structure of the model under the
260  root tree (a detailed description is given in section 3: Code  root tree (a detailed description is given in section 3: Code
261  structure).  structure).
262    
263  \begin{itemize}  \begin{itemize}
264    
265  \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.  
266        
267  \item \textit{diags}: contains the code relative to time-averaged  \item \texttt{eesupp}: contains the execution environment source code.
268    diagnostics. It is subdivided into two subdirectories \textit{inc}    Also subdivided into two subdirectories \texttt{inc} and
269    and \textit{src} that contain include files (*.\textit{h} files) and    \texttt{src}.
270    Fortran subroutines (*.\textit{F} files), respectively.    
271    \item \texttt{model}: this directory contains the main source code.
272  \item \textit{doc}: contains brief documentation notes.    Also subdivided into two subdirectories \texttt{inc} and
273        \texttt{src}.
 \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.  
274        
275  \item \textit{model}: this directory contains the main source code.  \item \texttt{pkg}: contains the source code for the packages. Each
276    Also subdivided into two subdirectories \textit{inc} and    package corresponds to a subdirectory. For example, \texttt{gmredi}
   \textit{src}.  
     
 \item \textit{pkg}: contains the source code for the packages. Each  
   package corresponds to a subdirectory. For example, \textit{gmredi}  
277    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
278    \textit{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
279    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in chapter \ref{chap.packagesI}.
280        
281  \item \textit{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
282    For example, \textit{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
283    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
284    \textit{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
285    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
286    The latter is described in details in part V.    The latter is described in detail in part \ref{chap.ecco}.
287      This directory also contains the subdirectory build\_options, which
288      contains the `optfiles' with the compiler options for the different
289      compilers and machines that can run MITgcm.
290        
291  \item \textit{utils}: this directory contains various utilities. The  \item \texttt{utils}: this directory contains various utilities. The
292    subdirectory \textit{knudsen2} contains code and a makefile that    subdirectory \texttt{knudsen2} contains code and a makefile that
293    compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
294    formula for an ocean nonlinear equation of state. The    formula for an ocean nonlinear equation of state. The
295    \textit{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
296    model output directly into matlab. \textit{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
297    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
298    model output.    model output. The subdirectory exch2 contains the code needed for
299      the exch2 package to work with different combinations of domain
300      decompositions.
301        
302  \item \textit{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
303    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sect:modelExamples}.
304    
305  \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.  
     
 \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.  
306        
307  \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.  
308        
309  \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux  \item \texttt{optim}: Interface between MITgcm and line search code.
   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}.  
310        
 \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.  
311  \end{itemize}  \end{itemize}
312    
313  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}  
314  \label{sect:buildingCode}  \label{sect:buildingCode}
315    \begin{rawhtml}
316  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
317  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
318  compiler and optimization options and also figures out any file  
319  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
320  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
321    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
322    file dependencies. We supply a script (\texttt{genmake2}), described
323    in section \ref{sect:genmake}, that automatically creates the
324    \texttt{Makefile} for you. You then need to build the dependencies and
325  compile the code.  compile the code.
326    
327  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
328  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
329  actually do this but here let's build the code in  actually do this but here let's build the code in
330  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
331  \begin{verbatim}  \begin{verbatim}
332  % cd verification/exp2/input  % cd verification/exp2/build
333  \end{verbatim}  \end{verbatim}
334  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
335  \begin{verbatim}  \begin{verbatim}
336  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
337  \end{verbatim}  \end{verbatim}
338  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
339  code with any files in the directory {\em ./code/}.  code with any files in the directory \texttt{../code/}.
340    
341  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
342  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
343  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
344  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
345    tools/build\_options} directory.  Under some circumstances, a user  the \texttt{tools/build\_options} directory.  Under some
346  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
347  combination of compiler, compiler flags, libraries, and other options  specify the exact combination of compiler, compiler flags, libraries,
348  necessary to build a particular configuration of MITgcm.  In such  and other options necessary to build a particular configuration of
349  cases, it is generally helpful to read the existing ``optfiles'' and  MITgcm.  In such cases, it is generally helpful to read the existing
350  mimic their syntax.  ``optfiles'' and mimic their syntax.
351    
352  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
353  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
354  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
355  architectures) to the  architectures) to the
356  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
357  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
358  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
359  list.  list.
360    
361  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
362  \begin{verbatim}  \begin{verbatim}
363  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
364  \end{verbatim}  \end{verbatim}
365    
366  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
367    dependencies with the command:
368  \begin{verbatim}  \begin{verbatim}
369  % make depend  % make depend
370  \end{verbatim}  \end{verbatim}
371  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
372  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
373  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
374    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
375  directory.  this directory.  It is important to note that the {\tt make depend}
376    stage will occasionally produce warnings or errors since the
377    dependency parsing tool is unable to find all of the necessary header
378    files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
379    is usually OK to ignore the warnings/errors and proceed to the next
380    step.
381    
382  Next compile the code:  Next one can compile the code using:
383  \begin{verbatim}  \begin{verbatim}
384  % make  % make
385  \end{verbatim}  \end{verbatim}
386  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
387  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
388  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
389    (shared multi-processor) systems, the build process can often be sped
390    up appreciably using the command:
391    \begin{verbatim}
392    % make -j 2
393    \end{verbatim}
394    where the ``2'' can be replaced with a number that corresponds to the
395    number of CPUs available.
396    
397  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
398  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
399    first creating links to all the input files:
400    \begin{verbatim}
401    ln -s ../input/* .
402    \end{verbatim}
403    and then calling the executable with:
404  \begin{verbatim}  \begin{verbatim}
405  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
406  \end{verbatim}  \end{verbatim}
407  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
408  output.txt}.  \texttt{output.txt}.
   
409    
410  \subsection{Building/compiling the code elsewhere}  \subsection{Building/compiling the code elsewhere}
411    
# Line 666  the one experiment: Line 512  the one experiment:
512  \end{verbatim}  \end{verbatim}
513    
514    
515    \subsection{Using \texttt{genmake2}}
 \subsection{Using \textit{genmake2}}  
516  \label{sect:genmake}  \label{sect:genmake}
517    
518  To compile the code, first use the program \texttt{genmake2} (located  To compile the code, first use the program \texttt{genmake2} (located
519  in the \textit{tools} directory) to generate a Makefile.  in the \texttt{tools} directory) to generate a Makefile.
520  \texttt{genmake2} is a shell script written to work with all  \texttt{genmake2} is a shell script written to work with all
521  ``sh''--compatible shells including bash v1, bash v2, and Bourne.  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
522  Internally, \texttt{genmake2} determines the locations of needed  %Internally, \texttt{genmake2} determines the locations of needed
523  files, the compiler, compiler options, libraries, and Unix tools.  It  %files, the compiler, compiler options, libraries, and Unix tools.  It
524  relies upon a number of ``optfiles'' located in the {\em  %relies upon a number of ``optfiles'' located in the
525    tools/build\_options} directory.  %\texttt{tools/build\_options} directory.
526    \texttt{genmake2} parses information from the following sources:
527    \begin{description}
528    \item[-] a {\em gemake\_local} file if one is found in the current
529      directory
530    \item[-] command-line options
531    \item[-] an "options file" as specified by the command-line option
532      \texttt{--optfile=/PATH/FILENAME}
533    \item[-] a {\em packages.conf} file (if one is found) with the
534      specific list of packages to compile. The search path for
535      file {\em packages.conf} is, first, the current directory and
536      then each of the "MODS" directories in the given order (see below).
537    \end{description}
538    
539    \subsubsection{Optfiles in \texttt{tools/build\_options} directory:}
540    
541  The purpose of the optfiles is to provide all the compilation options  The purpose of the optfiles is to provide all the compilation options
542  for particular ``platforms'' (where ``platform'' roughly means the  for particular ``platforms'' (where ``platform'' roughly means the
# Line 750  for inclusion.  Please send the file to Line 609  for inclusion.  Please send the file to
609  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
610  mailing list.  mailing list.
611    
612    \subsubsection{Command-line options:}
613    
614  In addition to the optfiles, \texttt{genmake2} supports a number of  In addition to the optfiles, \texttt{genmake2} supports a number of
615  helpful command-line options.  A complete list of these options can be  helpful command-line options.  A complete list of these options can be
616  obtained from:  obtained from:
# Line 772  The most important command-line options Line 633  The most important command-line options
633    the user's path.  When these three items have been identified,    the user's path.  When these three items have been identified,
634    genmake2 will try to find an optfile that has a matching name.    genmake2 will try to find an optfile that has a matching name.
635        
636    \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
637      directories containing ``modifications''.  These directories contain
638      files with names that may (or may not) exist in the main MITgcm
639      source tree but will be overridden by any identically-named sources
640      within the ``MODS'' directories.
641      
642      The order of precedence for this "name-hiding" is as follows:
643      \begin{itemize}
644      \item ``MODS'' directories (in the order given)
645      \item Packages either explicitly specified or provided by default
646        (in the order given)
647      \item Packages included due to package dependencies (in the order
648        that that package dependencies are parsed)
649      \item The "standard dirs" (which may have been specified by the
650        ``-standarddirs'' option)
651      \end{itemize}
652      
653    \item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
654      where package groups are defined. If not set, the package-groups
655      definition will be read from {\em pkg/pkg\_groups}.
656      It also contains the default list of packages (defined
657      as the group ``{\it default\_pkg\_list}'' which is used
658      when no specific package list ({\em packages.conf})
659      is found in current directory or in any "MODS" directory.
660    
661  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
662    used for packages.    used for packages.
663        
# Line 784  The most important command-line options Line 670  The most important command-line options
670    assumed that the two packages are compatible and will function    assumed that the two packages are compatible and will function
671    either with or without each other.    either with or without each other.
672        
 \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}  
     
673  \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or  \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
674    automatic differentiation options file to be used.  The file is    automatic differentiation options file to be used.  The file is
675    analogous to the ``optfile'' defined above but it specifies    analogous to the ``optfile'' defined above but it specifies
# Line 802  The most important command-line options Line 682  The most important command-line options
682    "STAF" compiler.  As with any compilers, it is helpful to have their    "STAF" compiler.  As with any compilers, it is helpful to have their
683    directories listed in your {\tt \$PATH} environment variable.    directories listed in your {\tt \$PATH} environment variable.
684        
685  \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of  \item[\texttt{--mpi}] This option enables certain MPI features (using
686    directories containing ``modifications''.  These directories contain    CPP \texttt{\#define}s) within the code and is necessary for MPI
687    files with names that may (or may not) exist in the main MITgcm    builds (see Section \ref{sect: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}  
688        
689  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
690    soft-links and other bugs common with the \texttt{make} versions    soft-links and other bugs common with the \texttt{make} versions
# Line 831  The most important command-line options Line 698  The most important command-line options
698    a Bourne, POSIX, or compatible) shell.  The syntax in these    a Bourne, POSIX, or compatible) shell.  The syntax in these
699    circumstances is:    circumstances is:
700    \begin{center}    \begin{center}
701      \texttt{/bin/sh genmake2 -bash=/bin/sh [...options...]}      \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
702    \end{center}    \end{center}
703    where \texttt{/bin/sh} can be replaced with the full path and name    where \texttt{/bin/sh} can be replaced with the full path and name
704    of the desired shell.    of the desired shell.
# Line 839  The most important command-line options Line 706  The most important command-line options
706  \end{description}  \end{description}
707    
708    
709    \subsection{Building with MPI}
710    \label{sect:mpi-build}
711    
712  \section{Running the model}  Building MITgcm to use MPI libraries can be complicated due to the
713  \label{sect:runModel}  variety of different MPI implementations available, their dependencies
714    or interactions with different compilers, and their often ad-hoc
715    locations within file systems.  For these reasons, its generally a
716    good idea to start by finding and reading the documentation for your
717    machine(s) and, if necessary, seeking help from your local systems
718    administrator.
719    
720  If compilation finished succesfuully (section \ref{sect:buildModel})  The steps for building MITgcm with MPI support are:
721  then an executable called {\em mitgcmuv} will now exist in the local  \begin{enumerate}
722  directory.    
723    \item Determine the locations of your MPI-enabled compiler and/or MPI
724      libraries and put them into an options file as described in Section
725      \ref{sect:genmake}.  One can start with one of the examples in:
726      \begin{rawhtml} <A
727        href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
728      \end{rawhtml}
729      \begin{center}
730        \texttt{MITgcm/tools/build\_options/}
731      \end{center}
732      \begin{rawhtml} </A> \end{rawhtml}
733      such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
734      \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
735      hand.  You may need help from your user guide or local systems
736      administrator to determine the exact location of the MPI libraries.
737      If libraries are not installed, MPI implementations and related
738      tools are available including:
739      \begin{itemize}
740      \item \begin{rawhtml} <A
741          href="http://www-unix.mcs.anl.gov/mpi/mpich/">
742        \end{rawhtml}
743        MPICH
744        \begin{rawhtml} </A> \end{rawhtml}
745    
746      \item \begin{rawhtml} <A
747          href="http://www.lam-mpi.org/">
748        \end{rawhtml}
749        LAM/MPI
750        \begin{rawhtml} </A> \end{rawhtml}
751    
752      \item \begin{rawhtml} <A
753          href="http://www.osc.edu/~pw/mpiexec/">
754        \end{rawhtml}
755        MPIexec
756        \begin{rawhtml} </A> \end{rawhtml}
757      \end{itemize}
758      
759    \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
760      (see Section \ref{sect:genmake}) using commands such as:
761    {\footnotesize \begin{verbatim}
762      %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
763      %  make depend
764      %  make
765    \end{verbatim} }
766      
767    \item Run the code with the appropriate MPI ``run'' or ``exec''
768      program provided with your particular implementation of MPI.
769      Typical MPI packages such as MPICH will use something like:
770    \begin{verbatim}
771      %  mpirun -np 4 -machinefile mf ./mitgcmuv
772    \end{verbatim}
773      Sightly more complicated scripts may be needed for many machines
774      since execution of the code may be controlled by both the MPI
775      library and a job scheduling and queueing system such as PBS,
776      LoadLeveller, Condor, or any of a number of similar tools.  A few
777      example scripts (those used for our \begin{rawhtml} <A
778        href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
779      verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
780      at:
781      \begin{rawhtml} <A
782        href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/">
783      \end{rawhtml}
784      {\footnotesize \tt
785        http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
786      \begin{rawhtml} </A> \end{rawhtml}
787      or at:
788      \begin{rawhtml} <A
789        href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
790      \end{rawhtml}
791      {\footnotesize \tt
792        http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
793      \begin{rawhtml} </A> \end{rawhtml}
794    
795  To run the model as a single process (ie. not in parallel) simply  \end{enumerate}
796  type:  
797    An example of the above process on the MITgcm cluster (``cg01'') using
798    the GNU g77 compiler and the mpich MPI library is:
799    
800    {\footnotesize \begin{verbatim}
801      %  cd MITgcm/verification/exp5
802      %  mkdir build
803      %  cd build
804      %  ../../../tools/genmake2 -mpi -mods=../code \
805           -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
806      %  make depend
807      %  make
808      %  cd ../input
809      %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
810           -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
811    \end{verbatim} }
812    
813    \section[Running MITgcm]{Running the model in prognostic mode}
814    \label{sect:runModel}
815    \begin{rawhtml}
816    <!-- CMIREDIR:runModel: -->
817    \end{rawhtml}
818    
819    If compilation finished succesfully (section \ref{sect:buildingCode})
820    then an executable called \texttt{mitgcmuv} will now exist in the
821    local directory.
822    
823    To run the model as a single process (\textit{ie.} not in parallel)
824    simply type:
825  \begin{verbatim}  \begin{verbatim}
826  % ./mitgcmuv  % ./mitgcmuv
827  \end{verbatim}  \end{verbatim}
# Line 858  do!). The above command will spew out ma Line 831  do!). The above command will spew out ma
831  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
832  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
833  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
834  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
835  \begin{verbatim}  \begin{verbatim}
836  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
837  \end{verbatim}  \end{verbatim}
838    In the event that the model encounters an error and stops, it is very
839  For the example experiments in {\em verification}, an example of the  helpful to include the last few line of this \texttt{output.txt} file
840  output is kept in {\em results/output.txt} for comparison. You can compare  along with the (\texttt{stderr}) error message within any bug reports.
841  your {\em output.txt} with this one to check that the set-up works.  
842    For the example experiments in \texttt{verification}, an example of the
843    output is kept in \texttt{results/output.txt} for comparison. You can
844    compare your \texttt{output.txt} with the corresponding one for that
845    experiment to check that the set-up works.
846    
847    
848    
849  \subsection{Output files}  \subsection{Output files}
850    
851  The model produces various output files. At a minimum, the instantaneous  The model produces various output files and, when using \texttt{mnc},
852  ``state'' of the model is written out, which is made of the following files:  sometimes even directories.  Depending upon the I/O package(s)
853    selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
854    both as determined by \texttt{code/packages.conf}) and the run-time
855    flags set (in \texttt{input/data.pkg}), the following output may
856    appear.
857    
858    
859    \subsubsection{MDSIO output files}
860    
861    The ``traditional'' output files are generated by the \texttt{mdsio}
862    package.  At a minimum, the instantaneous ``state'' of the model is
863    written out, which is made of the following files:
864    
865  \begin{itemize}  \begin{itemize}
866  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
867  0 $ eastward).    and positive eastward).
868    
869  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
870  and $> 0$ northward).    (m/s and positive northward).
871    
872  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
873  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
874  i.e. downward).    towards increasing pressure i.e. downward).
875    
876  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
877  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
878    
879  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
880  (g/kg).    vapor (g/kg).
881    
882  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
883  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
884  \end{itemize}  \end{itemize}
885    
886  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
887  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
888  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
889    
890  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
891    
892  \begin{itemize}  \begin{itemize}
893  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
894  \end{itemize}  \end{itemize}
895    
896  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 910  form and is used for restarting the inte Line 898  form and is used for restarting the inte
898  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
899    
900  \begin{itemize}  \begin{itemize}
901  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
902  \end{itemize}  \end{itemize}
903    
904  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
905  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
906  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
907  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
908  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
909  output to save disk space during long integrations.  output to save disk space during long integrations.
910    
911    \subsubsection{MNC output files}
912    
913    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
914    is usually (though not necessarily) placed within a subdirectory with
915    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  
916    
917  \subsection{Looking at the output}  \subsection{Looking at the output}
918    
919  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
920  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
921  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \texttt{.data} and \texttt{.meta}. The
922  binary form (big\_endian by default). The \textit{.meta} file is a  \texttt{.data} file contains the data written in binary form
923  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
924  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
925  particularly useful when running multi-processors calculations. The base  \texttt{.data} file. This way of organizing the output is particularly
926  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
927  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
928  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
929  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}
930    reads the data. Look at the comments inside the script to see how to
931    use it.
932    
933  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
934  \begin{verbatim}  \begin{verbatim}
# Line 949  Some examples of reading and visualizing Line 945  Some examples of reading and visualizing
945  >> 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
946  \end{verbatim}  \end{verbatim}
947    
948  \section{Doing it yourself: customizing the code}  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
949    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}  
950    
951  In this section, we only focus for now on the parameters that you are  The MNC output files are all in the ``self-describing'' netCDF
952  likely to change, i.e. the ones relative to forcing and dissipation  format and can thus be browsed and/or plotted using tools such as:
953  for example.  The details relevant to the vector-invariant form of the  \begin{itemize}
954  equations and the various advection schemes are not covered for the  \item \texttt{ncdump} is a utility which is typically included
955  moment. We assume that you use the standard form of the momentum    with every netCDF install:
956  equations (i.e. the flux-form) with the default advection scheme.    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
957  Also, there are a few logical variables that allow you to turn on/off  \begin{verbatim}
958  various terms in the momentum equation. These variables are called  http://www.unidata.ucar.edu/packages/netcdf/
959  \textbf{momViscosity, momAdvection, momForcing, useCoriolis,  \end{verbatim}
960    momPressureForcing, momStepping} and \textbf{metricTerms }and are    \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
961  assumed to be set to \texttt{'.TRUE.'} here.  Look at the file    binaries into formatted ASCII text files.
 \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}  
   
 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).  
962    
963  \begin{description}  \item \texttt{ncview} utility is a very convenient and quick way
964  \item[run duration] \    to plot netCDF data and it runs on most OSes:
965      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
966    \begin{verbatim}
967    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
968    \end{verbatim}
969      \begin{rawhtml} </A> \end{rawhtml}
970        
971    The beginning of a simulation is set by specifying a start time (in  \item MatLAB(c) and other common post-processing environments provide
972    s) through the real variable \textbf{startTime} or by specifying an    various netCDF interfaces including:
973    initial iteration number through the integer variable    \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
974    \textbf{nIter0}. If these variables are set to nonzero values, the  \begin{verbatim}
975    model will look for a ''pickup'' file \textit{pickup.0000nIter0} to  http://mexcdf.sourceforge.net/
976    restart the integration. The end of a simulation is set through the  \end{verbatim}
977    real variable \textbf{endTime} (in s).  Alternatively, you can    \begin{rawhtml} </A> \end{rawhtml}
978    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}
979    integer variable \textbf{nTimeSteps}.  \begin{verbatim}
980    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
981  \item[frequency of output] \  \end{verbatim}
982        \begin{rawhtml} </A> \end{rawhtml}
983    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}  
   
984    
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