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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  A web site is maintained for release 2 (``Pelican'') of MITgcm:  <!-- CMIREDIR:whereToFindInfo: -->
20  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}  \end{rawhtml}
21  \begin{verbatim}  
22  http://mitgcm.org/pelican  There is a web-archived support mailing list for the model that
23  \end{verbatim}  you can email at \texttt{MITgcm-support@mitgcm.org} after subscribing to:
24  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} <A href=http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
 Here you will find an on-line version of this document, a  
 ``browsable'' copy of the code and a searchable database of the model  
 and site, as well as links for downloading the model and  
 documentation, to data-sources, and other related sites.  
   
 There is also a web-archived support mailing list for the model that  
 you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:  
 \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}  
25  \begin{verbatim}  \begin{verbatim}
26  http://mitgcm.org/mailman/listinfo/mitgcm-support/  http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support/
 http://mitgcm.org/pipermail/mitgcm-support/  
27  \end{verbatim}  \end{verbatim}
28  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
29  Essentially all of the MITgcm web pages can be searched using a  or browse at:
30  popular web crawler such as Google or through our own search facility:  \begin{rawhtml} <A href=http://mailman.mitgcm.org/pipermail/mitgcm-support/ target="idontexist"> \end{rawhtml}
 \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}  
31  \begin{verbatim}  \begin{verbatim}
32  http://mitgcm.org/htdig/  http://mailman.mitgcm.org/pipermail/mitgcm-support/
33  \end{verbatim}  \end{verbatim}
34  \begin{rawhtml} </A> \end{rawhtml}  \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}  
   
 %% 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.  
315    
316  \subsection{Full list of model examples}  \item \texttt{verification}: this directory contains the model
317      examples. See section \ref{sec:modelExamples}.
318    
319  \begin{enumerate}  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
     
 \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}  
320    
321  \subsection{Directory structure of model examples}  \item \texttt{lsopt}: Line search code used for optimization.
   
 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:  
322    
323    \begin{itemize}  \item \texttt{optim}: Interface between MITgcm and line search code.
   \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 (``optfiles'') contained in  appropriate set of options from the files (``optfiles'') contained in
359  the {\em tools/build\_options} directory.  Under some circumstances, a  the \texttt{tools/build\_options} directory.  Under some
360  user may have to create a new ``optfile'' in order to specify the  circumstances, a user may have to create a new ``optfile'' in order to
361  exact combination of compiler, compiler flags, libraries, and other  specify the exact combination of compiler, compiler flags, libraries,
362  options necessary to build a particular configuration of MITgcm.  In  and other options necessary to build a particular configuration of
363  such cases, it is generally helpful to read the existing ``optfiles''  MITgcm.  In such cases, it is generally helpful to read the existing
364  and 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.  It is important to note that the {\tt make depend} stage  this directory.  It is important to note that the {\tt make depend}
390  will occasionally produce warnings or errors since the dependency  stage will occasionally produce warnings or errors since the
391  parsing tool is unable to find all of the necessary header files  dependency parsing tool is unable to find all of the necessary header
392  (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it is  files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
393  usually OK to ignore the warnings/errors and proceed to the next step.  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}
425    
426    In the example above (section \ref{sec:buildingCode}) we built the
427    executable in the {\em input} directory of the experiment for
428    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
430    entire source tree. The only requirement to do so is you have {\tt
431      genmake2} in your path or you know the absolute path to {\tt
432      genmake2}.
433    
434    The following sections outline some possible methods of organizing
435    your source and data.
436    
437    \subsubsection{Building from the {\em ../code directory}}
438    
439    This is just as simple as building in the {\em input/} directory:
440    \begin{verbatim}
441    % cd verification/exp2/code
442    % ../../../tools/genmake2
443    % make depend
444    % make
445    \end{verbatim}
446    However, to run the model the executable ({\em mitgcmuv}) and input
447    files must be in the same place. If you only have one calculation to make:
448    \begin{verbatim}
449    % cd ../input
450    % cp ../code/mitgcmuv ./
451    % ./mitgcmuv > output.txt
452    \end{verbatim}
453    or if you will be making multiple runs with the same executable:
454    \begin{verbatim}
455    % cd ../
456    % cp -r input run1
457    % cp code/mitgcmuv run1
458    % cd run1
459    % ./mitgcmuv > output.txt
460    \end{verbatim}
461    
462    \subsubsection{Building from a new directory}
463    
464    Since the {\em input} directory contains input files it is often more
465    useful to keep {\em input} pristine and build in a new directory
466    within {\em verification/exp2/}:
467    \begin{verbatim}
468    % cd verification/exp2
469    % mkdir build
470    % cd build
471    % ../../../tools/genmake2 -mods=../code
472    % make depend
473    % make
474    \end{verbatim}
475    This builds the code exactly as before but this time you need to copy
476    either the executable or the input files or both in order to run the
477    model. For example,
478    \begin{verbatim}
479    % cp ../input/* ./
480    % ./mitgcmuv > output.txt
481    \end{verbatim}
482    or if you tend to make multiple runs with the same executable then
483    running in a new directory each time might be more appropriate:
484    \begin{verbatim}
485    % cd ../
486    % mkdir run1
487    % cp build/mitgcmuv run1/
488    % cp input/* run1/
489    % cd run1
490    % ./mitgcmuv > output.txt
491    \end{verbatim}
492    
493    \subsubsection{Building on a scratch disk}
494    
495    Model object files and output data can use up large amounts of disk
496    space so it is often the case that you will be operating on a large
497    scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
498    following commands will build the model in {\em /scratch/exp2-run1}:
499    \begin{verbatim}
500    % cd /scratch/exp2-run1
501    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
502      -mods=~/MITgcm/verification/exp2/code
503    % make depend
504    % make
505    \end{verbatim}
506    To run the model here, you'll need the input files:
507    \begin{verbatim}
508    % cp ~/MITgcm/verification/exp2/input/* ./
509    % ./mitgcmuv > output.txt
510    \end{verbatim}
511    
512    As before, you could build in one directory and make multiple runs of
513    the one experiment:
514    \begin{verbatim}
515    % cd /scratch/exp2
516    % mkdir build
517    % cd build
518    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
519      -mods=~/MITgcm/verification/exp2/code
520    % make depend
521    % make
522    % cd ../
523    % cp -r ~/MITgcm/verification/exp2/input run2
524    % cd run2
525    % ./mitgcmuv > output.txt
526    \end{verbatim}
527    
528    \subsection{Using \texttt{genmake2}}
529    \label{sec:genmake}
530    
531    To compile the code, first use the program \texttt{genmake2} (located
532    in the \texttt{tools} directory) to generate a Makefile.
533    \texttt{genmake2} is a shell script written to work with all
534    ``sh''--compatible shells including bash v1, bash v2, and Bourne.
535    %Internally, \texttt{genmake2} determines the locations of needed
536    %files, the compiler, compiler options, libraries, and Unix tools.  It
537    %relies upon a number of ``optfiles'' located in the
538    %\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
555    for particular ``platforms'' (where ``platform'' roughly means the
556    combination of the hardware and the compiler) and code configurations.
557    Given the combinations of possible compilers and library dependencies
558    ({\it eg.}  MPI and NetCDF) there may be numerous optfiles available
559    for a single machine.  The naming scheme for the majority of the
560    optfiles shipped with the code is
561    \begin{center}
562      {\bf OS\_HARDWARE\_COMPILER }
563    \end{center}
564    where
565    \begin{description}
566    \item[OS] is the name of the operating system (generally the
567      lower-case output of the {\tt 'uname'} command)
568    \item[HARDWARE] is a string that describes the CPU type and
569      corresponds to output from the  {\tt 'uname -m'} command:
570      \begin{description}
571      \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
572        and athlon
573      \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
574      \item[amd64] is AMD x86\_64 systems
575      \item[ppc] is for Mac PowerPC systems
576      \end{description}
577    \item[COMPILER] is the compiler name (generally, the name of the
578      FORTRAN executable)
579    \end{description}
580    
581    In many cases, the default optfiles are sufficient and will result in
582    usable Makefiles.  However, for some machines or code configurations,
583    new ``optfiles'' must be written. To create a new optfile, it is
584    generally best to start with one of the defaults and modify it to suit
585    your needs.  Like \texttt{genmake2}, the optfiles are all written
586    using a simple ``sh''--compatible syntax.  While nearly all variables
587    used within \texttt{genmake2} may be specified in the optfiles, the
588    critical ones that should be defined are:
589    
590    \begin{description}
591    \item[FC] the FORTRAN compiler (executable) to use
592    \item[DEFINES] the command-line DEFINE options passed to the compiler
593    \item[CPP] the C pre-processor to use
594    \item[NOOPTFLAGS] options flags for special files that should not be
595      optimized
596    \end{description}
597    
598    For example, the optfile for a typical Red Hat Linux machine (``ia32''
599    architecture) using the GCC (g77) compiler is
600    \begin{verbatim}
601    FC=g77
602    DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
603    CPP='cpp  -traditional -P'
604    NOOPTFLAGS='-O0'
605    #  For IEEE, use the "-ffloat-store" option
606    if test "x$IEEE" = x ; then
607        FFLAGS='-Wimplicit -Wunused -Wuninitialized'
608        FOPTIM='-O3 -malign-double -funroll-loops'
609    else
610        FFLAGS='-Wimplicit -Wunused -ffloat-store'
611        FOPTIM='-O0 -malign-double'
612    fi
613    \end{verbatim}
614    
615    If you write an optfile for an unrepresented machine or compiler, you
616    are strongly encouraged to submit the optfile to the MITgcm project
617    for inclusion.  Please send the file to the
618    \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
619    \begin{center}
620      MITgcm-support@mitgcm.org
621    \end{center}
622    \begin{rawhtml} </A> \end{rawhtml}
623    mailing list.
624    
625    \subsubsection{Command-line options:}
626    
627    In addition to the optfiles, \texttt{genmake2} supports a number of
628    helpful command-line options.  A complete list of these options can be
629    obtained from:
630    \begin{verbatim}
631    % genmake2 -h
632    \end{verbatim}
633    
634    The most important command-line options are:
635    \begin{description}
636    
637    \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
638      should be used for a particular build.
639    
640      If no "optfile" is specified (either through the command line or the
641      MITGCM\_OPTFILE environment variable), genmake2 will try to make a
642      reasonable guess from the list provided in {\em
643        tools/build\_options}.  The method used for making this guess is
644      to first determine the combination of operating system and hardware
645      (eg. "linux\_ia32") and then find a working FORTRAN compiler within
646      the user's path.  When these three items have been identified,
647      genmake2 will try to find an optfile that has a matching name.
648    
649    \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
650      directories containing ``modifications''.  These directories contain
651      files with names that may (or may not) exist in the main MITgcm
652      source tree but will be overridden by any identically-named sources
653      within the ``MODS'' directories.
654    
655      The order of precedence for this "name-hiding" is as follows:
656      \begin{itemize}
657      \item ``MODS'' directories (in the order given)
658      \item Packages either explicitly specified or provided by default
659        (in the order given)
660      \item Packages included due to package dependencies (in the order
661        that that package dependencies are parsed)
662      \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
675      used for packages.
676    
677      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
679      where each line containes either a comment ("\#") or a simple
680      "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol
681      specifies a "must be used with" or a "must not be used with"
682      relationship, respectively.  If no rule is specified, then it is
683      assumed that the two packages are compatible and will function
684      either with or without each other.
685    
686    \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
687      automatic differentiation options file to be used.  The file is
688      analogous to the ``optfile'' defined above but it specifies
689      information for the AD build process.
690    
691      The default file is located in {\em
692        tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
693      and "TAMC" compilers.  An alternate version is also available at
694      {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
695      "STAF" compiler.  As with any compilers, it is helpful to have their
696      directories listed in your {\tt \$PATH} environment variable.
697    
698    \item[\texttt{--mpi}] This option enables certain MPI features (using
699      CPP \texttt{\#define}s) within the code and is necessary for MPI
700      builds (see Section \ref{sec:mpi-build}).
701    
702    \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
703      soft-links and other bugs common with the \texttt{make} versions
704      provided by commercial Unix vendors, GNU \texttt{make} (sometimes
705      called \texttt{gmake}) should be preferred.  This option provides a
706      means for specifying the make executable to be used.
707    
708    \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
709      machines, the ``bash'' shell is unavailable.  To run on these
710      systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
711      a Bourne, POSIX, or compatible) shell.  The syntax in these
712      circumstances is:
713      \begin{center}
714        \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
715      \end{center}
716      where \texttt{/bin/sh} can be replaced with the full path and name
717      of the desired shell.
718    
719    \end{description}
720    
721    \subsection{Building with MPI}
722    \label{sec:mpi-build}
723    
724    Building MITgcm to use MPI libraries can be complicated due to the
725    variety of different MPI implementations available, their dependencies
726    or interactions with different compilers, and their often ad-hoc
727    locations within file systems.  For these reasons, its generally a
728    good idea to start by finding and reading the documentation for your
729    machine(s) and, if necessary, seeking help from your local systems
730    administrator.
731    
732    The steps for building MITgcm with MPI support are:
733    \begin{enumerate}
734    
735    \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
737      \ref{sec:genmake}.  One can start with one of the examples in:
738      \begin{rawhtml} <A
739        href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
740      \end{rawhtml}
741      \begin{center}
742        \texttt{MITgcm/tools/build\_options/}
743      \end{center}
744      \begin{rawhtml} </A> \end{rawhtml}
745      such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
746      \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
747      hand.  You may need help from your user guide or local systems
748      administrator to determine the exact location of the MPI libraries.
749      If libraries are not installed, MPI implementations and related
750      tools are available including:
751      \begin{itemize}
752      \item \begin{rawhtml} <A
753          href="http://www-unix.mcs.anl.gov/mpi/mpich/">
754        \end{rawhtml}
755        MPICH
756        \begin{rawhtml} </A> \end{rawhtml}
757    
758      \item \begin{rawhtml} <A
759          href="http://www.lam-mpi.org/">
760        \end{rawhtml}
761        LAM/MPI
762        \begin{rawhtml} </A> \end{rawhtml}
763    
764      \item \begin{rawhtml} <A
765          href="http://www.osc.edu/~pw/mpiexec/">
766        \end{rawhtml}
767        MPIexec
768        \begin{rawhtml} </A> \end{rawhtml}
769      \end{itemize}
770    
771    \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
772      (see Section \ref{sec:genmake}) using commands such as:
773    {\footnotesize \begin{verbatim}
774      %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
775      %  make depend
776      %  make
777    \end{verbatim} }
778    
779    \item Run the code with the appropriate MPI ``run'' or ``exec''
780      program provided with your particular implementation of MPI.
781      Typical MPI packages such as MPICH will use something like:
782    \begin{verbatim}
783      %  mpirun -np 4 -machinefile mf ./mitgcmuv
784    \end{verbatim}
785      Sightly more complicated scripts may be needed for many machines
786      since execution of the code may be controlled by both the MPI
787      library and a job scheduling and queueing system such as PBS,
788      LoadLeveller, Condor, or any of a number of similar tools.  A few
789      example scripts (those used for our \begin{rawhtml} <A
790        href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
791      verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
792      at:
793      \begin{rawhtml} <A
794        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}
803      {\footnotesize \tt
804        http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
805      \begin{rawhtml} </A> \end{rawhtml}
806    
807    \end{enumerate}
808    
809    An example of the above process on the MITgcm cluster (``cg01'') using
810    the GNU g77 compiler and the mpich MPI library is:
811    
812    {\footnotesize \begin{verbatim}
813      %  cd MITgcm/verification/exp5
814      %  mkdir build
815      %  cd build
816      %  ../../../tools/genmake2 -mpi -mods=../code \
817           -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
818      %  make depend
819      %  make
820      %  cd ../input
821      %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
822           -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
823    \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    
# Line 583  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}
# Line 591  In the event that the model encounters a Line 851  In the event that the model encounters a
851  helpful to include the last few line of this \texttt{output.txt} file  helpful to include the last few line of this \texttt{output.txt} file
852  along with the (\texttt{stderr}) error message within any bug reports.  along with the (\texttt{stderr}) error message within any bug reports.
853    
854  For the example experiments in {\em verification}, an example of the  For the example experiments in \texttt{verification}, an example of the
855  output is kept in {\em results/output.txt} for comparison. You can  output is kept in \texttt{results/output.txt} for comparison. You can
856  compare your {\em output.txt} with the corresponding one for that  compare your \texttt{output.txt} with the corresponding one for that
857  experiment to check that the set-up works.  experiment to check that the set-up works.
858    
   
   
859  \subsection{Output files}  \subsection{Output files}
860    
861  The model produces various output files.  Depending upon the I/O  The model produces various output files and, when using \texttt{mnc},
862  package selected (either \texttt{mdsio} or \texttt{mnc} or both as  sometimes even directories.  Depending upon the I/O package(s)
863  determined by both the compile-time settings and the run-time flags in  selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
864  \texttt{data.pkg}), the following output may appear.  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}  \subsubsection{MDSIO output files}
869    
# Line 613  package.  At a minimum, the instantaneou Line 872  package.  At a minimum, the instantaneou
872  written out, which is made of the following files:  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 648  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}  \subsubsection{MNC output files}
921    
922  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
923  is usually (though not necessarily) placed within a subdirectory with  is usually (though not necessarily) placed within a subdirectory with
924  a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files  a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.
 within this subdirectory are all in the ``self-describing'' netCDF  
 format and can thus be browsed and/or plotted using tools such as:  
 \begin{itemize}  
 \item At a minimum, the \texttt{ncdump} utility is typically included  
   with every netCDF install:  
   \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}  
 \begin{verbatim}  
 http://www.unidata.ucar.edu/packages/netcdf/  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml}  
   
 \item The \texttt{ncview} utility is a very convenient and quick way  
   to plot netCDF data and it runs on most OSes:  
   \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}  
 \begin{verbatim}  
 http://meteora.ucsd.edu/~pierce/ncview_home_page.html  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml}  
     
 \item MatLAB(c) and other common post-processing environments provide  
   various netCDF interfaces including:  
   \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}  
 \begin{verbatim}  
 http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml}  
   
 \end{itemize}  
   
925    
926  \subsection{Looking at the output}  \subsection{Looking at the output}
927    
928  The ``traditional'' or mdsio model data are written according to a  The ``traditional'' or mdsio model data are written according to a
929  ``meta/data'' file format.  Each variable is associated with two files  ``meta/data'' file format.  Each variable is associated with two files
930  with suffix names \textit{.data} and \textit{.meta}. The  with suffix names \texttt{.data} and \texttt{.meta}. The
931  \textit{.data} file contains the data written in binary form  \texttt{.data} file contains the data written in binary form
932  (big\_endian by default). The \textit{.meta} file is a ``header'' file  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
933  that contains information about the size and the structure of the  that contains information about the size and the structure of the
934  \textit{.data} file. This way of organizing the output is particularly  \texttt{.data} file. This way of organizing the output is particularly
935  useful when running multi-processors calculations. The base version of  useful when running multi-processors calculations. The base version of
936  the model includes a few matlab utilities to read output files written  the model includes a few matlab utilities to read output files written
937  in this format. The matlab scripts are located in the directory  in this format. The matlab scripts are located in the directory
938  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m}  \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  reads the data. Look at the comments inside the script to see how to
940  use it.  use it.
941    
# Line 726  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.  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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