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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{sec: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
23  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}  you can email at \texttt{MITgcm-support@mitgcm.org} after subscribing to:
24    \begin{rawhtml} <A href=http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
25  \begin{verbatim}  \begin{verbatim}
26  http://mitgcm.org/pelican  http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support/
27  \end{verbatim}  \end{verbatim}
28  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
29  Here you will find an on-line version of this document, a  or browse at:
30  ``browsable'' copy of the code and a searchable database of the model  \begin{rawhtml} <A href=http://mailman.mitgcm.org/pipermail/mitgcm-support/ target="idontexist"> \end{rawhtml}
 and site, as well as links for downloading the model and  
 documentation, to data-sources, and other related sites.  
   
 There is also a web-archived support mailing list for the model that  
 you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:  
 \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}  
31  \begin{verbatim}  \begin{verbatim}
32  http://mitgcm.org/mailman/listinfo/mitgcm-support/  http://mailman.mitgcm.org/pipermail/mitgcm-support/
 http://mitgcm.org/pipermail/mitgcm-support/  
33  \end{verbatim}  \end{verbatim}
34  \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  
   
   
35    
36  \section{Obtaining the code}  \section{Obtaining the code}
37  \label{sect:obtainingCode}  \label{sec:obtainingCode}
38    \begin{rawhtml}
39    <!-- CMIREDIR:obtainingCode: -->
40    \end{rawhtml}
41    
42  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
43  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 80  provide easy support for maintenance upd Line 68  provide easy support for maintenance upd
68  \end{enumerate}  \end{enumerate}
69    
70  \subsection{Method 1 - Checkout from CVS}  \subsection{Method 1 - Checkout from CVS}
71  \label{sect:cvs_checkout}  \label{sec:cvs_checkout}
72    
73  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
74  provides an efficient and elegant way of organizing your code and keeping  provides an efficient and elegant way of organizing your code and keeping
# Line 88  track of your changes. If CVS is not ava Line 76  track of your changes. If CVS is not ava
76  download a tar file.  download a tar file.
77    
78  Before you can use CVS, the following environment variable(s) should  Before you can use CVS, the following environment variable(s) should
79  be set within your shell.  For a csh or tcsh shell, put the following  be set within your shell.  For a csh or tcsh shell, put the following
80  \begin{verbatim}  \begin{verbatim}
81  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
82  \end{verbatim}  \end{verbatim}
83  in your .cshrc or .tcshrc file.  For bash or sh shells, put:  in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
84    shells, put:
85  \begin{verbatim}  \begin{verbatim}
86  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
87  \end{verbatim}  \end{verbatim}
88  in your \texttt{.profile} or \texttt{.bashrc} file.  in your \texttt{.profile} or \texttt{.bashrc} file.
89    
   
90  To get MITgcm through CVS, first register with the MITgcm CVS server  To get MITgcm through CVS, first register with the MITgcm CVS server
91  using command:  using command:
92  \begin{verbatim}  \begin{verbatim}
# Line 108  You only need to do a ``cvs login'' once Line 96  You only need to do a ``cvs login'' once
96    
97  To obtain the latest sources type:  To obtain the latest sources type:
98  \begin{verbatim}  \begin{verbatim}
99  % cvs co MITgcm  % cvs co -P MITgcm
100  \end{verbatim}  \end{verbatim}
101  or to get a specific release type:  or to get a specific release type:
102  \begin{verbatim}  \begin{verbatim}
103  % cvs co -P -r checkpoint52i_post  MITgcm  % cvs co -P -r checkpoint52i_post MITgcm
104  \end{verbatim}  \end{verbatim}
105    The CVS command ``\texttt{cvs co}'' is the abreviation of the full-name
106    ``\texttt{cvs checkout}'' command and using the option ``-P'' (\texttt{cvs co -P})
107    will prevent to download unnecessary empty directories.
108    
109  The MITgcm web site contains further directions concerning the source  The MITgcm web site contains further directions concerning the source
110  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
111  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
112  development milestones:  development milestones:
113  \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}
114  \begin{verbatim}  \begin{verbatim}
115  http://mitgcm.org/source_code.html  http://mitgcm.org/viewvc/MITgcm/MITgcm/
116  \end{verbatim}  \end{verbatim}
117  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
118    
# Line 135  of CVS aliases Line 127  of CVS aliases
127      \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline      \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline
128      \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\      \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\
129      \texttt{MITgcm\_verif\_basic}      \texttt{MITgcm\_verif\_basic}
130      &  Source code plus a small set of the verification examples      &  Source code plus a small set of the verification examples
131      (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5},      (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5},
132      \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\      \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\
133      \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\      \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\
134      \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\      \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\
# Line 147  of CVS aliases Line 139  of CVS aliases
139    \label{tab:cvsModules}    \label{tab:cvsModules}
140  \end{table}  \end{table}
141    
142  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \texttt{MITgcm}. If
143  the directory \textit{MITgcm} exists this command updates your code  the directory \texttt{MITgcm} exists this command updates your code
144  based on the repository. Each directory in the source tree contains a  based on the repository. Each directory in the source tree contains a
145  directory \textit{CVS}. This information is required by CVS to keep  directory \texttt{CVS}. This information is required by CVS to keep
146  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
147  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
148  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
149  MITgcm code can be found  MITgcm code can be found
150  \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}
151  here  here
152  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}.
 .  
153  It is important to note that the CVS aliases in Table  It is important to note that the CVS aliases in Table
154  \ref{tab:cvsModules} cannot be used in conjunction with the CVS  \ref{tab:cvsModules} cannot be used in conjunction with the CVS
155  \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories  \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
156  they create can be changed to a different name following the check-out:  they create can be changed to a different name following the check-out:
157  \begin{verbatim}  \begin{verbatim}
158     %  cvs co MITgcm_verif_basic     %  cvs co -P MITgcm_verif_basic
159     %  mv MITgcm MITgcm_verif_basic     %  mv MITgcm MITgcm_verif_basic
160  \end{verbatim}  \end{verbatim}
161    
162    Note that it is possible to checkout code without ``cvs login'' and without
163  \subsection{Method 2 - Tar file download}  setting any shell environment variables by specifying the pserver name and
164  \label{sect:conventionalDownload}  password in one line, for example:
   
 If you do not have CVS on your system, you can download the model as a  
 tar file from the web site at:  
 \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  
165  \begin{verbatim}  \begin{verbatim}
166  http://mitgcm.org/download/     %  cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -P MITgcm
167  \end{verbatim}  \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.  
168    
169  \subsubsection{Upgrading from an earlier version}  \subsubsection{Upgrading from an earlier version}
170    
# Line 199  your copy instead of downloading the ent Line 176  your copy instead of downloading the ent
176  \end{verbatim}  \end{verbatim}
177  and then issue the cvs update command such as:  and then issue the cvs update command such as:
178  \begin{verbatim}  \begin{verbatim}
179  % cvs -q update -r checkpoint52i_post -d -P  % cvs -q update -d -P -r checkpoint52i_post
180  \end{verbatim}  \end{verbatim}
181  This will update the ``tag'' to ``checkpoint52i\_post'', add any new  This will update the ``tag'' to ``checkpoint52i\_post'', add any new
182  directories (-d) and remove any empty directories (-P). The -q option  directories (-d) and remove any empty directories (-P). The -q option
# Line 245  have run into a problem for which ``we h Line 222  have run into a problem for which ``we h
222  latest code'' and we haven't made a ``tag'' or ``release'' since that  latest code'' and we haven't made a ``tag'' or ``release'' since that
223  patch then you'll need to get the latest code:  patch then you'll need to get the latest code:
224  \begin{verbatim}  \begin{verbatim}
225  % cvs -q update -A -d -P  % cvs -q update -d -P -A
226  \end{verbatim}  \end{verbatim}
227  Unlike, the ``check-out'' and ``update'' procedures above, there is no  Unlike, the ``check-out'' and ``update'' procedures above, there is no
228  ``tag'' or release name. The -A tells CVS to upgrade to the  ``tag'' or release name. The -A tells CVS to upgrade to the
# Line 255  that you may only have part of a patch. Line 232  that you may only have part of a patch.
232  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
233  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
234    
235    \subsection{Method 2 - Tar file download}
236    \label{sec:conventionalDownload}
237    
238    If you do not have CVS on your system, you can download the model as a
239    tar file from the web site at:
240    \begin{rawhtml} <A href=http://mitgcm.org/download/ target="idontexist"> \end{rawhtml}
241    \begin{verbatim}
242    http://mitgcm.org/download/
243    \end{verbatim}
244    \begin{rawhtml} </A> \end{rawhtml}
245    The tar file still contains CVS information which we urge you not to
246    delete; even if you do not use CVS yourself the information can help
247    us if you should need to send us your copy of the code.  If a recent
248    tar file does not exist, then please contact the developers through
249    the
250    \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
251    MITgcm-support@mitgcm.org
252    \begin{rawhtml} </A> \end{rawhtml}
253    mailing list.
254    
255  \section{Model and directory structure}  \section{Model and directory structure}
256    \begin{rawhtml}
257    <!-- CMIREDIR:directory_structure: -->
258    \end{rawhtml}
259    
260  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
261  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 263  framework for grid-point models. MITgcmU
263  model that uses the framework. Under this structure the model is split  model that uses the framework. Under this structure the model is split
264  into execution environment support code and conventional numerical  into execution environment support code and conventional numerical
265  model code. The execution environment support code is held under the  model code. The execution environment support code is held under the
266  \textit{eesupp} directory. The grid point model code is held under the  \texttt{eesupp} directory. The grid point model code is held under the
267  \textit{model} directory. Code execution actually starts in the  \texttt{model} directory. Code execution actually starts in the
268  \textit{eesupp} routines and not in the \textit{model} routines. For  \texttt{eesupp} routines and not in the \texttt{model} routines. For
269  this reason the top-level \textit{MAIN.F} is in the  this reason the top-level \texttt{MAIN.F} is in the
270  \textit{eesupp/src} directory. In general, end-users should not need  \texttt{eesupp/src} directory. In general, end-users should not need
271  to worry about this level. The top-level routine for the numerical  to worry about this level. The top-level routine for the numerical
272  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
273  a brief description of the directory structure of the model under the  a brief description of the directory structure of the model under the
274  root tree (a detailed description is given in section 3: Code  root tree (a detailed description is given in section 3: Code
275  structure).  structure).
276    
277  \begin{itemize}  \begin{itemize}
278    
279  \item \textit{bin}: this directory is initially empty. It is the  \item \texttt{doc}: contains brief documentation notes.
280    default directory in which to compile the code.  
281      \item \texttt{eesupp}: contains the execution environment source code.
282  \item \textit{diags}: contains the code relative to time-averaged    Also subdivided into two subdirectories \texttt{inc} and
283    diagnostics. It is subdivided into two subdirectories \textit{inc}    \texttt{src}.
284    and \textit{src} that contain include files (*.\textit{h} files) and  
285    Fortran subroutines (*.\textit{F} files), respectively.  \item \texttt{model}: this directory contains the main source code.
286      Also subdivided into two subdirectories \texttt{inc} and
287  \item \textit{doc}: contains brief documentation notes.    \texttt{src}.
288      
289  \item \textit{eesupp}: contains the execution environment source code.  \item \texttt{pkg}: contains the source code for the packages. Each
290    Also subdivided into two subdirectories \textit{inc} and    package corresponds to a subdirectory. For example, \texttt{gmredi}
   \textit{src}.  
     
 \item \textit{exe}: this directory is initially empty. It is the  
   default directory in which to execute the code.  
     
 \item \textit{model}: this directory contains the main source code.  
   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}  
291    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
292    \textit{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
293    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in chapter \ref{chap:packagesI}.
294      
295  \item \textit{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
296    For example, \textit{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
297    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
298    \textit{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
299    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
300    The latter is described in details in part V.    The latter is described in detail in part \ref{chap.ecco}.
301        This directory also contains the subdirectory build\_options, which
302  \item \textit{utils}: this directory contains various utilities. The    contains the `optfiles' with the compiler options for the different
303    subdirectory \textit{knudsen2} contains code and a makefile that    compilers and machines that can run MITgcm.
304    
305    \item \texttt{utils}: this directory contains various utilities. The
306      subdirectory \texttt{knudsen2} contains code and a makefile that
307    compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
308    formula for an ocean nonlinear equation of state. The    formula for an ocean nonlinear equation of state. The
309    \textit{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
310    model output directly into matlab. \textit{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
311    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
312    model output.    model output. The subdirectory exch2 contains the code needed for
313        the exch2 package to work with different combinations of domain
314  \item \textit{verification}: this directory contains the model    decompositions.
   examples. See section \ref{sect:modelExamples}.  
   
 \end{itemize}  
   
 \section[MITgcm Example Experiments]{Example experiments}  
 \label{sect:modelExamples}  
315    
316  %% a set of twenty-four pre-configured numerical experiments  \item \texttt{verification}: this directory contains the model
317      examples. See section \ref{sec:modelExamples}.
318    
319  The MITgcm distribution comes with more than a dozen pre-configured  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
 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.  
320    
321  \subsection{Full list of model examples}  \item \texttt{lsopt}: Line search code used for optimization.
322    
323  \begin{enumerate}  \item \texttt{optim}: Interface between MITgcm and line search code.
     
 \item \textit{exp0} - single layer, ocean double gyre (barotropic with  
   free-surface). This experiment is described in detail in section  
   \ref{sect:eg-baro}.  
   
 \item \textit{exp1} - Four layer, ocean double gyre. This experiment  
   is described in detail in section \ref{sect:eg-baroc}.  
     
 \item \textit{exp2} - 4x4 degree global ocean simulation with steady  
   climatological forcing. This experiment is described in detail in  
   section \ref{sect:eg-global}.  
     
 \item \textit{exp4} - Flow over a Gaussian bump in open-water or  
   channel with open boundaries.  
     
 \item \textit{exp5} - Inhomogenously forced ocean convection in a  
   doubly periodic box.  
   
 \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for  
 Gent/McWilliams scheme). 2D (Y-Z).  
   
 \item \textit{internal wave} - Ocean internal wave forced by open  
   boundary conditions.  
     
 \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  
   scheme; 1 month integration  
     
 \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and  
   Suarez '94 forcing.  
     
 \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing.  
     
 \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing on the cubed sphere.  
     
 \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  
   Global Zonal Mean configuration, 1x64x5 resolution.  
     
 \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate  
   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).  
     
 \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  
   physics. 3D Equatorial Channel configuration.  
     
 \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.  
   Global configuration, on latitude longitude grid with 128x64x5 grid  
   points ($2.8^\circ{\rm degree}$ resolution).  
     
 \item \textit{adjustment.128x64x1} Barotropic adjustment problem on  
   latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on  
   cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \textit{advect\_cs} Two-dimensional passive advection test on  
   cube sphere grid.  
     
 \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive  
   advection test on Cartesian grid.  
     
 \item \textit{advect\_yz} Two-dimensional (vertical plane) passive  
   advection test on Cartesian grid.  
     
 \item \textit{carbon} Simple passive tracer experiment. Includes  
   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:  
324    
   \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.  
325  \end{itemize}  \end{itemize}
326    
 Once you have chosen the example you want to run, you are ready to  
 compile the code.  
   
327  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
328  \label{sect:buildingCode}  \label{sec:buildingCode}
329    \begin{rawhtml}
330  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
331  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
332  compiler and optimization options and also figures out any file  
333  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
334  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
335    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
336    file dependencies. We supply a script (\texttt{genmake2}), described
337    in section \ref{sec:genmake}, that automatically creates the
338    \texttt{Makefile} for you. You then need to build the dependencies and
339  compile the code.  compile the code.
340    
341  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
342  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
343  actually do this but here let's build the code in  actually do this but here let's build the code in
344  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
345  \begin{verbatim}  \begin{verbatim}
346  % cd verification/exp2/input  % cd verification/exp2/build
347  \end{verbatim}  \end{verbatim}
348  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
349  \begin{verbatim}  \begin{verbatim}
350  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
351  \end{verbatim}  \end{verbatim}
352  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
353  code with any files in the directory {\em ./code/}.  code with any files in the directory \texttt{../code/}.
354    
355  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
356  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
357  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
358  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
359    tools/build\_options} directory.  Under some circumstances, a user  the \texttt{tools/build\_options} directory.  Under some
360  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
361  combination of compiler, compiler flags, libraries, and other options  specify the exact combination of compiler, compiler flags, libraries,
362  necessary to build a particular configuration of MITgcm.  In such  and other options necessary to build a particular configuration of
363  cases, it is generally helpful to read the existing ``optfiles'' and  MITgcm.  In such cases, it is generally helpful to read the existing
364  mimic their syntax.  ``optfiles'' and mimic their syntax.
365    
366  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
367  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
368  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
369  architectures) to the  architectures) to the
370  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
371  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
372  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
373  list.  list.
374    
375  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
376  \begin{verbatim}  \begin{verbatim}
377  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
378  \end{verbatim}  \end{verbatim}
379    
380  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
381    dependencies with the command:
382  \begin{verbatim}  \begin{verbatim}
383  % make depend  % make depend
384  \end{verbatim}  \end{verbatim}
385  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
386  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
387  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
388    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
389  directory.  this directory.  It is important to note that the {\tt make depend}
390    stage will occasionally produce warnings or errors since the
391    dependency parsing tool is unable to find all of the necessary header
392    files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
393    is usually OK to ignore the warnings/errors and proceed to the next
394    step.
395    
396  Next compile the code:  Next one can compile the code using:
397  \begin{verbatim}  \begin{verbatim}
398  % make  % make
399  \end{verbatim}  \end{verbatim}
400  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
401  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
402  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
403    (shared multi-processor) systems, the build process can often be sped
404    up appreciably using the command:
405    \begin{verbatim}
406    % make -j 2
407    \end{verbatim}
408    where the ``2'' can be replaced with a number that corresponds to the
409    number of CPUs available.
410    
411  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
412  given in section \ref{sect:runModel}. Here, we can run the model with:  given in section \ref{sec:runModel}. Here, we can run the model by
413    first creating links to all the input files:
414    \begin{verbatim}
415    ln -s ../input/* .
416    \end{verbatim}
417    and then calling the executable with:
418  \begin{verbatim}  \begin{verbatim}
419  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
420  \end{verbatim}  \end{verbatim}
421  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
422  output.txt}.  \texttt{output.txt}.
   
423    
424  \subsection{Building/compiling the code elsewhere}  \subsection{Building/compiling the code elsewhere}
425    
426  In the example above (section \ref{sect:buildingCode}) we built the  In the example above (section \ref{sec:buildingCode}) we built the
427  executable in the {\em input} directory of the experiment for  executable in the {\em input} directory of the experiment for
428  convenience. You can also configure and compile the code in other  convenience. You can also configure and compile the code in other
429  locations, for example on a scratch disk with out having to copy the  locations, for example on a scratch disk with out having to copy the
# Line 665  the one experiment: Line 525  the one experiment:
525  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
526  \end{verbatim}  \end{verbatim}
527    
   
528  \subsection{Using \texttt{genmake2}}  \subsection{Using \texttt{genmake2}}
529  \label{sect:genmake}  \label{sec:genmake}
530    
531  To compile the code, first use the program \texttt{genmake2} (located  To compile the code, first use the program \texttt{genmake2} (located
532  in the \texttt{tools} directory) to generate a Makefile.  in the \texttt{tools} directory) to generate a Makefile.
533  \texttt{genmake2} is a shell script written to work with all  \texttt{genmake2} is a shell script written to work with all
534  ``sh''--compatible shells including bash v1, bash v2, and Bourne.  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
535  Internally, \texttt{genmake2} determines the locations of needed  %Internally, \texttt{genmake2} determines the locations of needed
536  files, the compiler, compiler options, libraries, and Unix tools.  It  %files, the compiler, compiler options, libraries, and Unix tools.  It
537  relies upon a number of ``optfiles'' located in the  %relies upon a number of ``optfiles'' located in the
538  \texttt{tools/build\_options} directory.  %\texttt{tools/build\_options} directory.
539    \texttt{genmake2} parses information from the following sources:
540    \begin{description}
541    \item[-] a {\em gemake\_local} file if one is found in the current
542      directory
543    \item[-] command-line options
544    \item[-] an "options file" as specified by the command-line option
545      \texttt{--optfile=/PATH/FILENAME}
546    \item[-] a {\em packages.conf} file (if one is found) with the
547      specific list of packages to compile. The search path for
548      file {\em packages.conf} is, first, the current directory and
549      then each of the "MODS" directories in the given order (see below).
550    \end{description}
551    
552    \subsubsection{Optfiles in \texttt{tools/build\_options} directory:}
553    
554  The purpose of the optfiles is to provide all the compilation options  The purpose of the optfiles is to provide all the compilation options
555  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 622  for inclusion.  Please send the file to
622  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
623  mailing list.  mailing list.
624    
625    \subsubsection{Command-line options:}
626    
627  In addition to the optfiles, \texttt{genmake2} supports a number of  In addition to the optfiles, \texttt{genmake2} supports a number of
628  helpful command-line options.  A complete list of these options can be  helpful command-line options.  A complete list of these options can be
629  obtained from:  obtained from:
# Line 758  obtained from: Line 633  obtained from:
633    
634  The most important command-line options are:  The most important command-line options are:
635  \begin{description}  \begin{description}
636      
637  \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that  \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
638    should be used for a particular build.    should be used for a particular build.
639      
640    If no "optfile" is specified (either through the command line or the    If no "optfile" is specified (either through the command line or the
641    MITGCM\_OPTFILE environment variable), genmake2 will try to make a    MITGCM\_OPTFILE environment variable), genmake2 will try to make a
642    reasonable guess from the list provided in {\em    reasonable guess from the list provided in {\em
# Line 770  The most important command-line options Line 645  The most important command-line options
645    (eg. "linux\_ia32") and then find a working FORTRAN compiler within    (eg. "linux\_ia32") and then find a working FORTRAN compiler within
646    the user's path.  When these three items have been identified,    the user's path.  When these three items have been identified,
647    genmake2 will try to find an optfile that has a matching name.    genmake2 will try to find an optfile that has a matching name.
648      
649  \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default  \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
650    set of packages to be used.  The normal order of precedence for    directories containing ``modifications''.  These directories contain
651    packages is as follows:    files with names that may (or may not) exist in the main MITgcm
652    \begin{enumerate}    source tree but will be overridden by any identically-named sources
653    \item If available, the command line (\texttt{--pdefault}) settings    within the ``MODS'' directories.
654      over-rule any others.  
655      The order of precedence for this "name-hiding" is as follows:
656    \item Next, \texttt{genmake2} will look for a file named    \begin{itemize}
657      ``\texttt{packages.conf}'' in the local directory or in any of the    \item ``MODS'' directories (in the order given)
658      directories specified with the \texttt{--mods} option.    \item Packages either explicitly specified or provided by default
659            (in the order given)
660    \item Finally, if neither of the above are available,    \item Packages included due to package dependencies (in the order
661      \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.      that that package dependencies are parsed)
662    \end{enumerate}    \item The "standard dirs" (which may have been specified by the
663          ``-standarddirs'' option)
664      \end{itemize}
665    
666    \item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
667      where package groups are defined. If not set, the package-groups
668      definition will be read from {\em pkg/pkg\_groups}.
669      It also contains the default list of packages (defined
670      as the group ``{\it default\_pkg\_list}'' which is used
671      when no specific package list ({\em packages.conf})
672      is found in current directory or in any "MODS" directory.
673    
674  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
675    used for packages.    used for packages.
676      
677    If not specified, the default dependency file {\em pkg/pkg\_depend}    If not specified, the default dependency file {\em pkg/pkg\_depend}
678    is used.  The syntax for this file is parsed on a line-by-line basis    is used.  The syntax for this file is parsed on a line-by-line basis
679    where each line containes either a comment ("\#") or a simple    where each line containes either a comment ("\#") or a simple
# Line 797  The most important command-line options Line 682  The most important command-line options
682    relationship, respectively.  If no rule is specified, then it is    relationship, respectively.  If no rule is specified, then it is
683    assumed that the two packages are compatible and will function    assumed that the two packages are compatible and will function
684    either with or without each other.    either with or without each other.
685      
686  \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or  \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
687    automatic differentiation options file to be used.  The file is    automatic differentiation options file to be used.  The file is
688    analogous to the ``optfile'' defined above but it specifies    analogous to the ``optfile'' defined above but it specifies
689    information for the AD build process.    information for the AD build process.
690      
691    The default file is located in {\em    The default file is located in {\em
692      tools/adjoint\_options/adjoint\_default} and it defines the "TAF"      tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
693    and "TAMC" compilers.  An alternate version is also available at    and "TAMC" compilers.  An alternate version is also available at
694    {\em tools/adjoint\_options/adjoint\_staf} that selects the newer    {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
695    "STAF" compiler.  As with any compilers, it is helpful to have their    "STAF" compiler.  As with any compilers, it is helpful to have their
696    directories listed in your {\tt \$PATH} environment variable.    directories listed in your {\tt \$PATH} environment variable.
697      
 \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}  
     
698  \item[\texttt{--mpi}] This option enables certain MPI features (using  \item[\texttt{--mpi}] This option enables certain MPI features (using
699    CPP \texttt{\#define}s) within the code and is necessary for MPI    CPP \texttt{\#define}s) within the code and is necessary for MPI
700    builds (see Section \ref{sect:mpi-build}).    builds (see Section \ref{sec:mpi-build}).
701      
702  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
703    soft-links and other bugs common with the \texttt{make} versions    soft-links and other bugs common with the \texttt{make} versions
704    provided by commercial Unix vendors, GNU \texttt{make} (sometimes    provided by commercial Unix vendors, GNU \texttt{make} (sometimes
705    called \texttt{gmake}) should be preferred.  This option provides a    called \texttt{gmake}) should be preferred.  This option provides a
706    means for specifying the make executable to be used.    means for specifying the make executable to be used.
707      
708  \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)  \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
709    machines, the ``bash'' shell is unavailable.  To run on these    machines, the ``bash'' shell is unavailable.  To run on these
710    systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,    systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
# Line 850  The most important command-line options Line 718  The most important command-line options
718    
719  \end{description}  \end{description}
720    
   
721  \subsection{Building with MPI}  \subsection{Building with MPI}
722  \label{sect:mpi-build}  \label{sec:mpi-build}
723    
724  Building MITgcm to use MPI libraries can be complicated due to the  Building MITgcm to use MPI libraries can be complicated due to the
725  variety of different MPI implementations available, their dependencies  variety of different MPI implementations available, their dependencies
# Line 864  administrator. Line 731  administrator.
731    
732  The steps for building MITgcm with MPI support are:  The steps for building MITgcm with MPI support are:
733  \begin{enumerate}  \begin{enumerate}
734      
735  \item Determine the locations of your MPI-enabled compiler and/or MPI  \item Determine the locations of your MPI-enabled compiler and/or MPI
736    libraries and put them into an options file as described in Section    libraries and put them into an options file as described in Section
737    \ref{sect:genmake}.  One can start with one of the examples in:    \ref{sec:genmake}.  One can start with one of the examples in:
738    \begin{rawhtml} <A    \begin{rawhtml} <A
739      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
740    \end{rawhtml}    \end{rawhtml}
741    \begin{center}    \begin{center}
742      \texttt{MITgcm/tools/build\_options/}      \texttt{MITgcm/tools/build\_options/}
# Line 900  The steps for building MITgcm with MPI s Line 767  The steps for building MITgcm with MPI s
767      MPIexec      MPIexec
768      \begin{rawhtml} </A> \end{rawhtml}      \begin{rawhtml} </A> \end{rawhtml}
769    \end{itemize}    \end{itemize}
770      
771  \item Build the code with the \texttt{genmake2} \texttt{-mpi} option  \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
772    (see Section \ref{sect:genmake}) using commands such as:    (see Section \ref{sec:genmake}) using commands such as:
773  {\footnotesize \begin{verbatim}  {\footnotesize \begin{verbatim}
774    %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE    %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
775    %  make depend    %  make depend
776    %  make    %  make
777  \end{verbatim} }  \end{verbatim} }
778      
779  \item Run the code with the appropriate MPI ``run'' or ``exec''  \item Run the code with the appropriate MPI ``run'' or ``exec''
780    program provided with your particular implementation of MPI.    program provided with your particular implementation of MPI.
781    Typical MPI packages such as MPICH will use something like:    Typical MPI packages such as MPICH will use something like:
# Line 920  The steps for building MITgcm with MPI s Line 787  The steps for building MITgcm with MPI s
787    library and a job scheduling and queueing system such as PBS,    library and a job scheduling and queueing system such as PBS,
788    LoadLeveller, Condor, or any of a number of similar tools.  A few    LoadLeveller, Condor, or any of a number of similar tools.  A few
789    example scripts (those used for our \begin{rawhtml} <A    example scripts (those used for our \begin{rawhtml} <A
790      href="http://mitgcm.org/testing.html"> \end{rawhtml}regular      href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
791    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
792    at:    at:
793    \begin{rawhtml} <A    \begin{rawhtml} <A
794      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/">
795      \end{rawhtml}
796      {\footnotesize \tt
797        http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
798      \begin{rawhtml} </A> \end{rawhtml}
799      or at:
800      \begin{rawhtml} <A
801        href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
802    \end{rawhtml}    \end{rawhtml}
803    {\footnotesize \tt    {\footnotesize \tt
804      http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }      http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
805    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
806    
807  \end{enumerate}  \end{enumerate}
# Line 948  the GNU g77 compiler and the mpich MPI l Line 822  the GNU g77 compiler and the mpich MPI l
822         -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv         -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
823  \end{verbatim} }  \end{verbatim} }
824    
   
   
825  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
826  \label{sect:runModel}  \label{sec:runModel}
827    \begin{rawhtml}
828    <!-- CMIREDIR:runModel: -->
829    \end{rawhtml}
830    
831  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sec:buildingCode})
832  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
833  local directory.  local directory.
834    
835  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)
836  type:  simply type:
837  \begin{verbatim}  \begin{verbatim}
838  % ./mitgcmuv  % ./mitgcmuv
839  \end{verbatim}  \end{verbatim}
# Line 968  do!). The above command will spew out ma Line 843  do!). The above command will spew out ma
843  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
844  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
845  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
846  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
847  \begin{verbatim}  \begin{verbatim}
848  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
849  \end{verbatim}  \end{verbatim}
850    In the event that the model encounters an error and stops, it is very
851  For the example experiments in {\em verification}, an example of the  helpful to include the last few line of this \texttt{output.txt} file
852  output is kept in {\em results/output.txt} for comparison. You can compare  along with the (\texttt{stderr}) error message within any bug reports.
853  your {\em output.txt} with this one to check that the set-up works.  
854    For the example experiments in \texttt{verification}, an example of the
855    output is kept in \texttt{results/output.txt} for comparison. You can
856    compare your \texttt{output.txt} with the corresponding one for that
857    experiment to check that the set-up works.
858    
859  \subsection{Output files}  \subsection{Output files}
860    
861  The model produces various output files. At a minimum, the instantaneous  The model produces various output files and, when using \texttt{mnc},
862  ``state'' of the model is written out, which is made of the following files:  sometimes even directories.  Depending upon the I/O package(s)
863    selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
864    both as determined by \texttt{code/packages.conf}) and the run-time
865    flags set (in \texttt{input/data.pkg}), the following output may
866    appear.
867    
868    \subsubsection{MDSIO output files}
869    
870    The ``traditional'' output files are generated by the \texttt{mdsio}
871    package.  At a minimum, the instantaneous ``state'' of the model is
872    written out, which is made of the following files:
873    
874  \begin{itemize}  \begin{itemize}
875  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
876  0 $ eastward).    and positive eastward).
877    
878  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
879  and $> 0$ northward).    (m/s and positive northward).
880    
881  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
882  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
883  i.e. downward).    towards increasing pressure i.e. downward).
884    
885  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
886  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
887    
888  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
889  (g/kg).    vapor (g/kg).
890    
891  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
892  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
893  \end{itemize}  \end{itemize}
894    
895  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
896  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
897  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
898    
899  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
900    
901  \begin{itemize}  \begin{itemize}
902  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
903  \end{itemize}  \end{itemize}
904    
905  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 1020  form and is used for restarting the inte Line 907  form and is used for restarting the inte
907  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
908    
909  \begin{itemize}  \begin{itemize}
910  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
911  \end{itemize}  \end{itemize}
912    
913  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
914  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
915  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
916  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
917  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
918  output to save disk space during long integrations.  output to save disk space during long integrations.
919    
920    \subsubsection{MNC output files}
921    
922    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
923    is usually (though not necessarily) placed within a subdirectory with
924    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.
925    
926  \subsection{Looking at the output}  \subsection{Looking at the output}
927    
928  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
929  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
930  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \texttt{.data} and \texttt{.meta}. The
931  binary form (big\_endian by default). The \textit{.meta} file is a  \texttt{.data} file contains the data written in binary form
932  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
933  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
934  particularly useful when running multi-processors calculations. The base  \texttt{.data} file. This way of organizing the output is particularly
935  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
936  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
937  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
938  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}
939    reads the data. Look at the comments inside the script to see how to
940    use it.
941    
942  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
943  \begin{verbatim}  \begin{verbatim}
# Line 1059  Some examples of reading and visualizing Line 954  Some examples of reading and visualizing
954  >> 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
955  \end{verbatim}  \end{verbatim}
956    
957    Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
958    they are described in Section \ref{sec:pkg:mnc}.
959    
960    The MNC output files are all in the ``self-describing'' netCDF
961    format and can thus be browsed and/or plotted using tools such as:
962    \begin{itemize}
963    \item \texttt{ncdump} is a utility which is typically included
964      with every netCDF install:
965      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
966    \begin{verbatim}
967    http://www.unidata.ucar.edu/packages/netcdf/
968    \end{verbatim}
969      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
970      binaries into formatted ASCII text files.
971    
972    \item \texttt{ncview} utility is a very convenient and quick way
973      to plot netCDF data and it runs on most OSes:
974      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
975    \begin{verbatim}
976    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
977    \end{verbatim}
978      \begin{rawhtml} </A> \end{rawhtml}
979    
980    \item MatLAB(c) and other common post-processing environments provide
981      various netCDF interfaces including:
982      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
983    \begin{verbatim}
984    http://mexcdf.sourceforge.net/
985    \end{verbatim}
986      \begin{rawhtml} </A> \end{rawhtml}
987      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
988    \begin{verbatim}
989    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
990    \end{verbatim}
991      \begin{rawhtml} </A> \end{rawhtml}
992    \end{itemize}
993    
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