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1  % $Header$  % $Header$
2  % $Name$  % $Name$
3    
4    %\section{Getting started}
5    
6  \begin{center}  In this section, we describe how to use the model. In the first
7  {\Large \textbf{Using the model}}  section, we provide enough information to help you get started with
8    the model. We believe the best way to familiarize yourself with the
9    model is to run the case study examples provided with the base
10    version. Information on how to obtain, compile, and run the code is
11    found there as well as a brief description of the model structure
12    directory and the case study examples.  The latter and the code
13    structure are described more fully in chapters
14    \ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in
15    this section, we provide information on how to customize the code when
16    you are ready to try implementing the configuration you have in mind.
17    
18  \vspace*{4mm}  \section{Where to find information}
19    \label{sect:whereToFindInfo}
20    
21  \vspace*{3mm} {\large July 2001}  A web site is maintained for release 2 (``Pelican'') of MITgcm:
22  \end{center}  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
23    \begin{verbatim}
24    http://mitgcm.org/pelican
25    \end{verbatim}
26    \begin{rawhtml} </A> \end{rawhtml}
27    Here you will find an on-line version of this document, a
28    ``browsable'' copy of the code and a searchable database of the model
29    and site, as well as links for downloading the model and
30    documentation, to data-sources, and other related sites.
31    
32    There is also a web-archived support mailing list for the model that
33    you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
34    \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
35    \begin{verbatim}
36    http://mitgcm.org/mailman/listinfo/mitgcm-support/
37    http://mitgcm.org/pipermail/mitgcm-support/
38    \end{verbatim}
39    \begin{rawhtml} </A> \end{rawhtml}
40    Essentially all of the MITgcm web pages can be searched using a
41    popular web crawler such as Google or through our own search facility:
42    \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}
43    \begin{verbatim}
44    http://mitgcm.org/htdig/
45    \end{verbatim}
46    \begin{rawhtml} </A> \end{rawhtml}
47    %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
48    
 In this part, we describe how to use the model. In the first section, we  
 provide enough information to help you get started with the model. We  
 believe the best way to familiarize yourself with the model is to run the  
 case study examples provided with the base version. Information on how to  
 obtain, compile, and run the code is found there as well as a brief  
 description of the model structure directory and the case study examples.  
 The latter and the code structure are described more fully in sections 2 and  
 3, respectively. In section 4, we provide information on how to customize  
 the code when you are ready to try implementing the configuration you have  
 in mind.  
49    
 \section{Getting started}  
50    
51  \subsection{Obtaining the code}  \section{Obtaining the code}
52    \label{sect:obtainingCode}
53    
54  The reference web site for the model is:  MITgcm can be downloaded from our system by following
55  \begin{verbatim}  the instructions below. As a courtesy we ask that you send e-mail to us at
56  http://mitgcm.org  \begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml}
57  \end{verbatim}  MITgcm-support@mitgcm.org
58    \begin{rawhtml} </A> \end{rawhtml}
59    to enable us to keep track of who's using the model and in what application.
60    You can download the model two ways:
61    
62    \begin{enumerate}
63    \item Using CVS software. CVS is a freely available source code management
64    tool. To use CVS you need to have the software installed. Many systems
65    come with CVS pre-installed, otherwise good places to look for
66    the software for a particular platform are
67    \begin{rawhtml} <A href=http://www.cvshome.org/ target="idontexist"> \end{rawhtml}
68    cvshome.org
69    \begin{rawhtml} </A> \end{rawhtml}
70    and
71    \begin{rawhtml} <A href=http://www.wincvs.org/ target="idontexist"> \end{rawhtml}
72    wincvs.org
73    \begin{rawhtml} </A> \end{rawhtml}
74    .
75    
76    \item Using a tar file. This method is simple and does not
77    require any special software. However, this method does not
78    provide easy support for maintenance updates.
79    
80  On this site, you can download the model as well as find useful information,  \end{enumerate}
 some of which might overlap with what is written here. There is also a  
 support news group for the model located at (send your message to \texttt{%  
 support@mitgcm.org}):  
 \begin{verbatim}  
 news://mitgcm.org/mitgcm.support  
 \end{verbatim}  
81    
82  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
83  provides an efficient and elegant way of organizing your code and keeping  provides an efficient and elegant way of organizing your code and keeping
84  track of your changes. If CVS is not available on your machine, you can also  track of your changes. If CVS is not available on your machine, you can also
85  download a tar file.  download a tar file.
86    
87  \subsubsection{using CVS}  Before you can use CVS, the following environment variable(s) should
88    be set within your shell.  For a csh or tcsh shell, put the following
89    \begin{verbatim}
90    % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
91    \end{verbatim}
92    in your .cshrc or .tcshrc file.  For bash or sh shells, put:
93    \begin{verbatim}
94    % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
95    \end{verbatim}
96    in your .profile or .bashrc file.
97    
98    
99  Before you can use CVS, the following environment variable has to be set in  To get MITgcm through CVS, first register with the MITgcm CVS server
100  your .cshrc or .tcshrc:  using command:
101  \begin{verbatim}  \begin{verbatim}
 % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack  
102  % cvs login ( CVS password: cvsanon )  % cvs login ( CVS password: cvsanon )
103  \end{verbatim}  \end{verbatim}
104    You only need to do a ``cvs login'' once.
105    
106  You only need to do ``cvs login'' once. To obtain the latest source:  To obtain the latest sources type:
107  \begin{verbatim}  \begin{verbatim}
108  % cvs co -d directory models/MITgcmUV  % cvs co MITgcm
109  \end{verbatim}  \end{verbatim}
110    or to get a specific release type:
111  This creates a directory called \textit{directory}. If \textit{directory}  \begin{verbatim}
112  exists this command updates your code based on the repository. Each  % cvs co -P -r checkpoint52i_post  MITgcm
113  directory in the source tree contains a directory \textit{CVS}. This  \end{verbatim}
114  information is required by CVS to keep track of your file versions with  The MITgcm web site contains further directions concerning the source
115  respect to the repository. Don't edit the files in \textit{CVS}! To obtain a  code and CVS.  It also contains a web interface to our CVS archive so
116  specific \textit{version} that is not the latest source:  that one may easily view the state of files, revisions, and other
117    development milestones:
118    \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
119  \begin{verbatim}  \begin{verbatim}
120  % cvs co -d directory -r version models/MITgcmUV  http://mitgcm.org/source\_code.html
121  \end{verbatim}  \end{verbatim}
122    \begin{rawhtml} </A> \end{rawhtml}
123    
 \subsubsection{other methods}  
124    
125  You can download the model as a tar file from the reference web site at:  The checkout process creates a directory called \textit{MITgcm}. If
126    the directory \textit{MITgcm} exists this command updates your code
127    based on the repository. Each directory in the source tree contains a
128    directory \textit{CVS}. This information is required by CVS to keep
129    track of your file versions with respect to the repository. Don't edit
130    the files in \textit{CVS}!  You can also use CVS to download code
131    updates.  More extensive information on using CVS for maintaining
132    MITgcm code can be found
133    \begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml}
134    here
135    \begin{rawhtml} </A> \end{rawhtml}
136    .
137    
138    
139    \paragraph*{Conventional download method}
140    \label{sect:conventionalDownload}
141    
142    If you do not have CVS on your system, you can download the model as a
143    tar file from the web site at:
144    \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
145  \begin{verbatim}  \begin{verbatim}
146  http://mitgcm.org/download/  http://mitgcm.org/download/
147  \end{verbatim}  \end{verbatim}
148    \begin{rawhtml} </A> \end{rawhtml}
149  \subsection{Model and directory structure}  The tar file still contains CVS information which we urge you not to
150    delete; even if you do not use CVS yourself the information can help
151  The ``numerical'' model is contained within a execution environment support  us if you should need to send us your copy of the code.  If a recent
152  wrapper. This wrapper is designed to provide a general framework for  tar file does not exist, then please contact the developers through
153  grid-point models. MITgcmUV is a specific numerical model that uses the  the MITgcm-support list.
154  framework. Under this structure the model is split into execution  
155  environment support code and conventional numerical model code. The  \paragraph*{Upgrading from an earlier version}
156  execution environment support code is held under the \textit{eesupp}  
157  directory. The grid point model code is held under the \textit{model}  If you already have an earlier version of the code you can ``upgrade''
158  directory. Code execution actually starts in the \textit{eesupp} routines  your copy instead of downloading the entire repository again. First,
159  and not in the \textit{model} routines. For this reason the top-level  ``cd'' (change directory) to the top of your working copy:
160    \begin{verbatim}
161    % cd MITgcm
162    \end{verbatim}
163    and then issue the cvs update command such as:
164    \begin{verbatim}
165    % cvs -q update -r checkpoint52i_post -d -P
166    \end{verbatim}
167    This will update the ``tag'' to ``checkpoint52i\_post'', add any new
168    directories (-d) and remove any empty directories (-P). The -q option
169    means be quiet which will reduce the number of messages you'll see in
170    the terminal. If you have modified the code prior to upgrading, CVS
171    will try to merge your changes with the upgrades. If there is a
172    conflict between your modifications and the upgrade, it will report
173    that file with a ``C'' in front, e.g.:
174    \begin{verbatim}
175    C model/src/ini_parms.F
176    \end{verbatim}
177    If the list of conflicts scrolled off the screen, you can re-issue the
178    cvs update command and it will report the conflicts. Conflicts are
179    indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and
180    ``$>>>>>>>$''. For example,
181    \begin{verbatim}
182    <<<<<<< ini_parms.F
183         & bottomDragLinear,myOwnBottomDragCoefficient,
184    =======
185         & bottomDragLinear,bottomDragQuadratic,
186    >>>>>>> 1.18
187    \end{verbatim}
188    means that you added ``myOwnBottomDragCoefficient'' to a namelist at
189    the same time and place that we added ``bottomDragQuadratic''. You
190    need to resolve this conflict and in this case the line should be
191    changed to:
192    \begin{verbatim}
193         & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
194    \end{verbatim}
195    and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted.
196    Unless you are making modifications which exactly parallel
197    developments we make, these types of conflicts should be rare.
198    
199    \paragraph*{Upgrading to the current pre-release version}
200    
201    We don't make a ``release'' for every little patch and bug fix in
202    order to keep the frequency of upgrades to a minimum. However, if you
203    have run into a problem for which ``we have already fixed in the
204    latest code'' and we haven't made a ``tag'' or ``release'' since that
205    patch then you'll need to get the latest code:
206    \begin{verbatim}
207    % cvs -q update -A -d -P
208    \end{verbatim}
209    Unlike, the ``check-out'' and ``update'' procedures above, there is no
210    ``tag'' or release name. The -A tells CVS to upgrade to the
211    very latest version. As a rule, we don't recommend this since you
212    might upgrade while we are in the processes of checking in the code so
213    that you may only have part of a patch. Using this method of updating
214    also means we can't tell what version of the code you are working
215    with. So please be sure you understand what you're doing.
216    
217    \section{Model and directory structure}
218    
219    The ``numerical'' model is contained within a execution environment
220    support wrapper. This wrapper is designed to provide a general
221    framework for grid-point models. MITgcmUV is a specific numerical
222    model that uses the framework. Under this structure the model is split
223    into execution environment support code and conventional numerical
224    model code. The execution environment support code is held under the
225    \textit{eesupp} directory. The grid point model code is held under the
226    \textit{model} directory. Code execution actually starts in the
227    \textit{eesupp} routines and not in the \textit{model} routines. For
228    this reason the top-level
229  \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,  \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,
230  end-users should not need to worry about this level. The top-level routine  end-users should not need to worry about this level. The top-level routine
231  for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%  for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%
# Line 97  directory in which to compile the code. Line 238  directory in which to compile the code.
238    
239  \item \textit{diags}: contains the code relative to time-averaged  \item \textit{diags}: contains the code relative to time-averaged
240  diagnostics. It is subdivided into two subdirectories \textit{inc} and  diagnostics. It is subdivided into two subdirectories \textit{inc} and
241  \textit{src} that contain include files (*.\textit{h} files) and fortran  \textit{src} that contain include files (*.\textit{h} files) and Fortran
242  subroutines (*.\textit{F} files), respectively.  subroutines (*.\textit{F} files), respectively.
243    
244  \item \textit{doc}: contains brief documentation notes.  \item \textit{doc}: contains brief documentation notes.
# Line 118  relative to the atmospheric intermediate Line 259  relative to the atmospheric intermediate
259  in detail in section 3.  in detail in section 3.
260    
261  \item \textit{tools}: this directory contains various useful tools. For  \item \textit{tools}: this directory contains various useful tools. For
262  example, \textit{genmake} is a script written in csh (C-shell) that should  example, \textit{genmake2} is a script written in csh (C-shell) that should
263  be used to generate your makefile. The directory \textit{adjoint} contains  be used to generate your makefile. The directory \textit{adjoint} contains
264  the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that  the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that
265  generates the adjoint code. The latter is described in details in part V.  generates the adjoint code. The latter is described in details in part V.
266    
267  \item \textit{utils}: this directory contains various utilities. The  \item \textit{utils}: this directory contains various utilities. The
268  subdirectory \textit{knudsen2} contains code and a makefile that compute  subdirectory \textit{knudsen2} contains code and a makefile that
269  coefficients of the polynomial approximation to the knudsen formula for an  compute coefficients of the polynomial approximation to the knudsen
270  ocean nonlinear equation of state. The \textit{matlab} subdirectory contains  formula for an ocean nonlinear equation of state. The \textit{matlab}
271  matlab scripts for reading model output directly into matlab. \textit{scripts%  subdirectory contains matlab scripts for reading model output directly
272  } contains C-shell post-processing scripts for joining processor-based and  into matlab. \textit{scripts} contains C-shell post-processing
273  tiled-based model output.  scripts for joining processor-based and tiled-based model output.
274    
275  \item \textit{verification}: this directory contains the model examples. See  \item \textit{verification}: this directory contains the model examples. See
276  below.  section \ref{sect:modelExamples}.
277  \end{itemize}  \end{itemize}
278    
279  \subsection{Model examples}  \section{Example experiments}
280    \label{sect:modelExamples}
281    
282    %% a set of twenty-four pre-configured numerical experiments
283    
284  Now that you have successfully downloaded the model code we recommend that  The MITgcm distribution comes with more than a dozen pre-configured
285  you first try to run the examples provided with the base version. You will  numerical experiments. Some of these example experiments are tests of
286  probably want to run the example that is the closest to the configuration  individual parts of the model code, but many are fully fledged
287  you will use eventually. The examples are located in subdirectories under  numerical simulations. A few of the examples are used for tutorial
288  the directory \textit{verification} and are briefly described below (a full  documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.
289  description is given in section 2):  The other examples follow the same general structure as the tutorial
290    examples. However, they only include brief instructions in a text file
291    called {\it README}.  The examples are located in subdirectories under
292    the directory \textit{verification}. Each example is briefly described
293    below.
294    
295  \subsubsection{List of model examples}  \subsection{Full list of model examples}
296    
297  \begin{itemize}  \begin{enumerate}
298  \item \textit{exp0} - single layer, ocean double gyre (barotropic with  \item \textit{exp0} - single layer, ocean double gyre (barotropic with
299  free-surface).    free-surface). This experiment is described in detail in section
300      \ref{sect:eg-baro}.
 \item \textit{exp1} - 4 layers, ocean double gyre.  
301    
302    \item \textit{exp1} - Four layer, ocean double gyre. This experiment
303      is described in detail in section \ref{sect:eg-baroc}.
304      
305  \item \textit{exp2} - 4x4 degree global ocean simulation with steady  \item \textit{exp2} - 4x4 degree global ocean simulation with steady
306  climatological forcing.    climatological forcing. This experiment is described in detail in
307      section \ref{sect:eg-global}.
308  \item \textit{exp4} - flow over a Gaussian bump in open-water or channel    
309  with open boundaries.  \item \textit{exp4} - Flow over a Gaussian bump in open-water or
310      channel with open boundaries.
311      
312    \item \textit{exp5} - Inhomogenously forced ocean convection in a
313      doubly periodic box.
314    
315  \item \textit{exp5} - inhomogenously forced ocean convection in a doubly  \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
 periodic box.  
   
 \item \textit{front\_relax} - relaxation of an ocean thermal front (test for  
316  Gent/McWilliams scheme). 2D (Y-Z).  Gent/McWilliams scheme). 2D (Y-Z).
317    
318  \item \textit{internal wave} - ocean internal wave forced by open boundary  \item \textit{internal wave} - Ocean internal wave forced by open
319  conditions.    boundary conditions.
320      
321  \item \textit{natl\_box} - eastern subtropical North Atlantic with KPP  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
322  scheme; 1 month integration    scheme; 1 month integration
323      
324  \item \textit{hs94.1x64x5} - zonal averaged atmosphere using Held and Suarez  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and
325  '94 forcing.    Suarez '94 forcing.
326      
327  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
328  '94 forcing.    Suarez '94 forcing.
329      
330  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
331  Suarez '94 forcing on the cubed sphere.    Suarez '94 forcing on the cubed sphere.
332      
333  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics, 5 layers  \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
334  Molteni physics package. Global Zonal Mean configuration, 1x64x5 resolution.    Global Zonal Mean configuration, 1x64x5 resolution.
335      
336  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
337  physics, 5 layers Molteni physics package. Equatorial Slice configuration.    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
338  2D (X-Z).    
   
339  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
340  physics, 5 layers Molteni physics package. 3D Equatorial Channel    physics. 3D Equatorial Channel configuration.
341  configuration (not completely tested).    
342    \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
343      Global configuration, on latitude longitude grid with 128x64x5 grid
344      points ($2.8^\circ{\rm degree}$ resolution).
345      
346    \item \textit{adjustment.128x64x1} Barotropic adjustment problem on
347      latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
348        degree}$ resolution).
349      
350    \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on
351      cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
352        degree}$ resolution).
353      
354    \item \textit{advect\_cs} Two-dimensional passive advection test on
355      cube sphere grid.
356      
357    \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive
358      advection test on Cartesian grid.
359      
360    \item \textit{advect\_yz} Two-dimensional (vertical plane) passive
361      advection test on Cartesian grid.
362      
363    \item \textit{carbon} Simple passive tracer experiment. Includes
364      derivative calculation. Described in detail in section
365      \ref{sect:eg-carbon-ad}.
366    
367    \item \textit{flt\_example} Example of using float package.
368      
369    \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux
370      boundary conditions and poles.
371    
372    \item \textit{global\_ocean\_pressure} Global circulation in pressure
373      coordinate (non-Boussinesq ocean model). Described in detail in
374      section \ref{sect:eg-globalpressure}.
375      
376    \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube
377      sphere grid.
378    
379  \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers  \end{enumerate}
 Molteni physics package. Global configuration, 128x64x5 resolution.  
380    
381  \item \textit{adjustment.128x64x1}  \subsection{Directory structure of model examples}
   
 \item \textit{adjustment.cs-32x32x1}  
 \end{itemize}  
   
 \subsubsection{Directory structure of model examples}  
382    
383  Each example directory has the following subdirectories:  Each example directory has the following subdirectories:
384    
385  \begin{itemize}  \begin{itemize}
386  \item \textit{code}: contains the code particular to the example. At a  \item \textit{code}: contains the code particular to the example. At a
387  minimum, this directory includes the following files:    minimum, this directory includes the following files:
388    
389  \begin{itemize}    \begin{itemize}
390  \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to the    \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
391  ``execution environment'' part of the code. The default version is located      the ``execution environment'' part of the code. The default
392  in \textit{eesupp/inc}.      version is located in \textit{eesupp/inc}.
393      
394      \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
395        the ``numerical model'' part of the code. The default version is
396        located in \textit{model/inc}.
397      
398      \item \textit{code/SIZE.h}: declares size of underlying
399        computational grid.  The default version is located in
400        \textit{model/inc}.
401      \end{itemize}
402      
403      In addition, other include files and subroutines might be present in
404      \textit{code} depending on the particular experiment. See Section 2
405      for more details.
406      
407    \item \textit{input}: contains the input data files required to run
408      the example. At a minimum, the \textit{input} directory contains the
409      following files:
410    
411      \begin{itemize}
412      \item \textit{input/data}: this file, written as a namelist,
413        specifies the main parameters for the experiment.
414      
415      \item \textit{input/data.pkg}: contains parameters relative to the
416        packages used in the experiment.
417      
418      \item \textit{input/eedata}: this file contains ``execution
419        environment'' data. At present, this consists of a specification
420        of the number of threads to use in $X$ and $Y$ under multithreaded
421        execution.
422      \end{itemize}
423    
424    In addition, you will also find in this directory the forcing and
425    topography files as well as the files describing the initial state of
426    the experiment.  This varies from experiment to experiment. See
427    section 2 for more details.
428    
429    \item \textit{results}: this directory contains the output file
430      \textit{output.txt} produced by the simulation example. This file is
431      useful for comparison with your own output when you run the
432      experiment.
433    \end{itemize}
434    
435  \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the  Once you have chosen the example you want to run, you are ready to compile
436  ``numerical model'' part of the code. The default version is located in  the code.
 \textit{model/inc}.  
437    
438  \item \textit{code/SIZE.h}: declares size of underlying computational grid.  \section{Building the code}
439  The default version is located in \textit{model/inc}.  \label{sect:buildingCode}
 \end{itemize}  
440    
441  In addition, other include files and subroutines might be present in \textit{%  To compile the code, we use the {\em make} program. This uses a file
442  code} depending on the particular experiment. See section 2 for more details.  ({\em Makefile}) that allows us to pre-process source files, specify
443    compiler and optimization options and also figures out any file
444    dependencies. We supply a script ({\em genmake2}), described in
445    section \ref{sect:genmake}, that automatically creates the {\em
446      Makefile} for you. You then need to build the dependencies and
447    compile the code.
448    
449    As an example, let's assume that you want to build and run experiment
450    \textit{verification/exp2}. The are multiple ways and places to
451    actually do this but here let's build the code in
452    \textit{verification/exp2/input}:
453    \begin{verbatim}
454    % cd verification/exp2/input
455    \end{verbatim}
456    First, build the {\em Makefile}:
457    \begin{verbatim}
458    % ../../../tools/genmake2 -mods=../code
459    \end{verbatim}
460    The command line option tells {\em genmake} to override model source
461    code with any files in the directory {\em ./code/}.
462    
463  \item \textit{input}: contains the input data files required to run the  On many systems, the {\em genmake2} program will be able to
464  example. At a mimimum, the \textit{input} directory contains the following  automatically recognize the hardware, find compilers and other tools
465  files:  within the user's path (``echo \$PATH''), and then choose an
466    appropriate set of options from the files contained in the {\em
467      tools/build\_options} directory.  Under some circumstances, a user
468    may have to create a new ``optfile'' in order to specify the exact
469    combination of compiler, compiler flags, libraries, and other options
470    necessary to build a particular configuration of MITgcm.  In such
471    cases, it is generally helpful to read the existing ``optfiles'' and
472    mimic their syntax.
473    
474    Through the MITgcm-support list, the MITgcm developers are willing to
475    provide help writing or modifing ``optfiles''.  And we encourage users
476    to post new ``optfiles'' (particularly ones for new machines or
477    architectures) to the MITgcm-support list.
478    
479  \begin{itemize}  To specify an optfile to {\em genmake2}, the syntax is:
480  \item \textit{input/data}: this file, written as a namelist, specifies the  \begin{verbatim}
481  main parameters for the experiment.  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
482    \end{verbatim}
483    
484  \item \textit{input/data.pkg}: contains parameters relative to the packages  Once a {\em Makefile} has been generated, we create the dependencies:
485  used in the experiment.  \begin{verbatim}
486    % make depend
487    \end{verbatim}
488    This modifies the {\em Makefile} by attaching a [long] list of files
489    upon which other files depend. The purpose of this is to reduce
490    re-compilation if and when you start to modify the code. The {\tt make
491      depend} command also creates links from the model source to this
492    directory.
493    
494  \item \textit{input/eedata}: this file contains ``execution environment''  Next compile the code:
495  data. At present, this consists of a specification of the number of threads  \begin{verbatim}
496  to use in $X$ and $Y$ under multithreaded execution.  % make
497  \end{itemize}  \end{verbatim}
498    The {\tt make} command creates an executable called \textit{mitgcmuv}.
499    Additional make ``targets'' are defined within the makefile to aid in
500    the production of adjoint and other versions of MITgcm.
501    
502  In addition, you will also find in this directory the forcing and topography  Now you are ready to run the model. General instructions for doing so are
503  files as well as the files describing the initial state of the experiment.  given in section \ref{sect:runModel}. Here, we can run the model with:
504  This varies from experiment to experiment. See section 2 for more details.  \begin{verbatim}
505    ./mitgcmuv > output.txt
506    \end{verbatim}
507    where we are re-directing the stream of text output to the file {\em
508    output.txt}.
509    
 \item \textit{results}: this directory contains the output file \textit{%  
 output.txt} produced by the simulation example. This file is useful for  
 comparison with your own output when you run the experiment.  
 \end{itemize}  
510    
511  Once you have chosen the example you want to run, you are ready to compile  \subsection{Building/compiling the code elsewhere}
512  the code.  
513    In the example above (section \ref{sect:buildingCode}) we built the
514    executable in the {\em input} directory of the experiment for
515    convenience. You can also configure and compile the code in other
516    locations, for example on a scratch disk with out having to copy the
517    entire source tree. The only requirement to do so is you have {\tt
518      genmake2} in your path or you know the absolute path to {\tt
519      genmake2}.
520    
521  \subsection{Compiling the code}  The following sections outline some possible methods of organizing
522    your source and data.
523    
524  \subsubsection{The script \textit{genmake}}  \subsubsection{Building from the {\em ../code directory}}
525    
526  To compile the code, use the script \textit{genmake} located in the \textit{%  This is just as simple as building in the {\em input/} directory:
 tools} directory. \textit{genmake} is a script that generates the makefile.  
 It has been written so that the code can be compiled on a wide diversity of  
 machines and systems. However, if it doesn't work the first time on your  
 platform, you might need to edit certain lines of \textit{genmake} in the  
 section containing the setups for the different machines. The file is  
 structured like this:  
 \begin{verbatim}  
         .  
         .  
         .  
 general instructions (machine independent)  
         .  
         .  
         .  
     - setup machine 1  
     - setup machine 2  
     - setup machine 3  
     - setup machine 4  
        etc  
         .  
         .  
         .  
 \end{verbatim}  
   
 For example, the setup corresponding to a DEC alpha machine is reproduced  
 here:  
 \begin{verbatim}  
   case OSF1+mpi:  
     echo "Configuring for DEC Alpha"  
     set CPP        = ( '/usr/bin/cpp -P' )  
     set DEFINES    = ( ${DEFINES}  '-DTARGET_DEC -DWORDLENGTH=1' )  
     set KPP        = ( 'kapf' )  
     set KPPFILES   = ( 'main.F' )  
     set KFLAGS1    = ( '-scan=132 -noconc -cmp=' )  
     set FC         = ( 'f77' )  
     set FFLAGS     = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' )  
     set FOPTIM     = ( '-O5 -fast -tune host -inline all' )  
     set NOOPTFLAGS = ( '-O0' )  
     set LIBS       = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' )  
     set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')  
     set RMFILES    = ( '*.p.out' )  
     breaksw  
 \end{verbatim}  
   
 Typically, these are the lines that you might need to edit to make \textit{%  
 genmake} work on your platform if it doesn't work the first time. \textit{%  
 genmake} understands several options that are described here:  
   
 \begin{itemize}  
 \item -rootdir=dir  
   
 indicates where the model root directory is relative to the directory where  
 you are compiling. This option is not needed if you compile in the \textit{%  
 bin} directory (which is the default compilation directory) or within the  
 \textit{verification} tree.  
   
 \item -mods=dir1,dir2,...  
   
 indicates the relative or absolute paths directories where the sources  
 should take precedence over the default versions (located in \textit{model},  
 \textit{eesupp},...). Typically, this option is used when running the  
 examples, see below.  
   
 \item -enable=pkg1,pkg2,...  
   
 enables packages source code \textit{pkg1}, \textit{pkg2},... when creating  
 the makefile.  
   
 \item -disable=pkg1,pkg2,...  
   
 disables packages source code \textit{pkg1}, \textit{pkg2},... when creating  
 the makefile.  
   
 \item -platform=machine  
   
 specifies the platform for which you want the makefile. In general, you  
 won't need this option. \textit{genmake} will select the right machine for  
 you (the one you're working on!). However, this option is useful if you have  
 a choice of several compilers on one machine and you want to use the one  
 that is not the default (ex: \texttt{pgf77} instead of \texttt{f77} under  
 Linux).  
   
 \item -mpi  
   
 this is used when you want to run the model in parallel processing mode  
 under mpi (see section on parallel computation for more details).  
   
 \item -jam  
   
 this is used when you want to run the model in parallel processing mode  
 under jam (see section on parallel computation for more details).  
 \end{itemize}  
   
 For some of the examples, there is a file called \textit{.genmakerc} in the  
 \textit{input} directory that has the relevant \textit{genmake} options for  
 that particular example. In this way you don't need to type the options when  
 invoking \textit{genmake}.  
   
 \subsubsection{Compiling}  
   
 Let's assume that you want to run, say, example \textit{exp2} in the \textit{%  
 input} directory. To compile the code, type the following commands from the  
 model root tree:  
527  \begin{verbatim}  \begin{verbatim}
528  % cd verification/exp2/input  % cd verification/exp2/code
529  % ../../../tools/genmake  % ../../../tools/genmake2
530  % make depend  % make depend
531  % make  % make
532  \end{verbatim}  \end{verbatim}
533    However, to run the model the executable ({\em mitgcmuv}) and input
534  If there is no \textit{.genmakerc} in the \textit{input} directory, you have  files must be in the same place. If you only have one calculation to make:
535  to use the following options when invoking \textit{genmake}:  \begin{verbatim}
536    % cd ../input
537    % cp ../code/mitgcmuv ./
538    % ./mitgcmuv > output.txt
539    \end{verbatim}
540    or if you will be making multiple runs with the same executable:
541  \begin{verbatim}  \begin{verbatim}
542  % ../../../tools/genmake  -mods=../code  % cd ../
543    % cp -r input run1
544    % cp code/mitgcmuv run1
545    % cd run1
546    % ./mitgcmuv > output.txt
547  \end{verbatim}  \end{verbatim}
548    
549  In addition, you will probably want to disable some of the packages. Taking  \subsubsection{Building from a new directory}
550  again the case of \textit{exp2}, the full \textit{genmake} command will  
551  probably look like this:  Since the {\em input} directory contains input files it is often more
552    useful to keep {\em input} pristine and build in a new directory
553    within {\em verification/exp2/}:
554    \begin{verbatim}
555    % cd verification/exp2
556    % mkdir build
557    % cd build
558    % ../../../tools/genmake2 -mods=../code
559    % make depend
560    % make
561    \end{verbatim}
562    This builds the code exactly as before but this time you need to copy
563    either the executable or the input files or both in order to run the
564    model. For example,
565  \begin{verbatim}  \begin{verbatim}
566  % ../../../tools/genmake  -mods=../code  -disable=kpp,gmredi,aim,...  % cp ../input/* ./
567    % ./mitgcmuv > output.txt
568    \end{verbatim}
569    or if you tend to make multiple runs with the same executable then
570    running in a new directory each time might be more appropriate:
571    \begin{verbatim}
572    % cd ../
573    % mkdir run1
574    % cp build/mitgcmuv run1/
575    % cp input/* run1/
576    % cd run1
577    % ./mitgcmuv > output.txt
578  \end{verbatim}  \end{verbatim}
579    
580  The make command creates an executable called \textit{mitgcmuv}.  \subsubsection{Building on a scratch disk}
581    
582  Note that you can compile and run the code in another directory than \textit{%  Model object files and output data can use up large amounts of disk
583  input}. You just need to make sure that you copy the input data files into  space so it is often the case that you will be operating on a large
584  the directory where you want to run the model. For example to compile from  scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
585  \textit{code}:  following commands will build the model in {\em /scratch/exp2-run1}:
586  \begin{verbatim}  \begin{verbatim}
587  % cd verification/exp2/code  % cd /scratch/exp2-run1
588  % ../../../tools/genmake  % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
589      -mods=~/MITgcm/verification/exp2/code
590    % make depend
591    % make
592    \end{verbatim}
593    To run the model here, you'll need the input files:
594    \begin{verbatim}
595    % cp ~/MITgcm/verification/exp2/input/* ./
596    % ./mitgcmuv > output.txt
597    \end{verbatim}
598    
599    As before, you could build in one directory and make multiple runs of
600    the one experiment:
601    \begin{verbatim}
602    % cd /scratch/exp2
603    % mkdir build
604    % cd build
605    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
606      -mods=~/MITgcm/verification/exp2/code
607  % make depend  % make depend
608  % make  % make
609    % cd ../
610    % cp -r ~/MITgcm/verification/exp2/input run2
611    % cd run2
612    % ./mitgcmuv > output.txt
613    \end{verbatim}
614    
615    
616    
617    \subsection{Using \textit{genmake2}}
618    \label{sect:genmake}
619    
620    To compile the code, first use the program \texttt{genmake2} (located
621    in the \textit{tools} directory) to generate a Makefile.
622    \texttt{genmake2} is a shell script written to work with all
623    ``sh''--compatible shells including bash v1, bash v2, and Bourne.
624    Internally, \texttt{genmake2} determines the locations of needed
625    files, the compiler, compiler options, libraries, and Unix tools.  It
626    relies upon a number of ``optfiles'' located in the {\em
627      tools/build\_options} directory.
628    
629    The purpose of the optfiles is to provide all the compilation options
630    for particular ``platforms'' (where ``platform'' roughly means the
631    combination of the hardware and the compiler) and code configurations.
632    Given the combinations of possible compilers and library dependencies
633    ({\it eg.}  MPI and NetCDF) there may be numerous optfiles available
634    for a single machine.  The naming scheme for the majority of the
635    optfiles shipped with the code is
636    \begin{center}
637      {\bf OS\_HARDWARE\_COMPILER }
638    \end{center}
639    where
640    \begin{description}
641    \item[OS] is the name of the operating system (generally the
642      lower-case output of the {\tt 'uname'} command)
643    \item[HARDWARE] is a string that describes the CPU type and
644      corresponds to output from the  {\tt 'uname -m'} command:
645      \begin{description}
646      \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
647        and athlon
648      \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
649      \item[amd64] is AMD x86\_64 systems
650      \item[ppc] is for Mac PowerPC systems
651      \end{description}
652    \item[COMPILER] is the compiler name (generally, the name of the
653      FORTRAN executable)
654    \end{description}
655    
656    In many cases, the default optfiles are sufficient and will result in
657    usable Makefiles.  However, for some machines or code configurations,
658    new ``optfiles'' must be written. To create a new optfile, it is
659    generally best to start with one of the defaults and modify it to suit
660    your needs.  Like \texttt{genmake2}, the optfiles are all written
661    using a simple ``sh''--compatible syntax.  While nearly all variables
662    used within \texttt{genmake2} may be specified in the optfiles, the
663    critical ones that should be defined are:
664    
665    \begin{description}
666    \item[FC] the FORTRAN compiler (executable) to use
667    \item[DEFINES] the command-line DEFINE options passed to the compiler
668    \item[CPP] the C pre-processor to use
669    \item[NOOPTFLAGS] options flags for special files that should not be
670      optimized
671    \end{description}
672    
673    For example, the optfile for a typical Red Hat Linux machine (``ia32''
674    architecture) using the GCC (g77) compiler is
675    \begin{verbatim}
676    FC=g77
677    DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
678    CPP='cpp  -traditional -P'
679    NOOPTFLAGS='-O0'
680    #  For IEEE, use the "-ffloat-store" option
681    if test "x$IEEE" = x ; then
682        FFLAGS='-Wimplicit -Wunused -Wuninitialized'
683        FOPTIM='-O3 -malign-double -funroll-loops'
684    else
685        FFLAGS='-Wimplicit -Wunused -ffloat-store'
686        FOPTIM='-O0 -malign-double'
687    fi
688  \end{verbatim}  \end{verbatim}
689    
690  \subsection{Running the model}  If you write an optfile for an unrepresented machine or compiler, you
691    are strongly encouraged to submit the optfile to the MITgcm project
692    for inclusion.  Please send the file to the
693    \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
694    \begin{center}
695      MITgcm-support@mitgcm.org
696    \end{center}
697    \begin{rawhtml} </A> \end{rawhtml}
698    mailing list.
699    
700  The first thing to do is to run the code by typing \textit{mitgcmuv} and see  In addition to the optfiles, \texttt{genmake2} supports a number of
701  what happens. You can compare what you get with what is in the \textit{%  helpful command-line options.  A complete list of these options can be
702  results} directory. Unless noted otherwise, most examples are set up to run  obtained from:
703  for a few time steps only so that you can quickly figure out whether the  \begin{verbatim}
704  model is working or not.  % genmake2 -h
705    \end{verbatim}
706    
707  \subsubsection{Output files}  The most important command-line options are:
708    \begin{description}
709      
710    \item[--optfile=/PATH/FILENAME] specifies the optfile that should be
711      used for a particular build.
712      
713      If no "optfile" is specified (either through the command line or the
714      MITGCM\_OPTFILE environment variable), genmake2 will try to make a
715      reasonable guess from the list provided in {\em
716        tools/build\_options}.  The method used for making this guess is
717      to first determine the combination of operating system and hardware
718      (eg. "linux\_ia32") and then find a working FORTRAN compiler within
719      the user's path.  When these three items have been identified,
720      genmake2 will try to find an optfile that has a matching name.
721      
722    \item[--pdepend=/PATH/FILENAME] specifies the dependency file used for
723      packages.
724      
725      If not specified, the default dependency file {\em pkg/pkg\_depend}
726      is used.  The syntax for this file is parsed on a line-by-line basis
727      where each line containes either a comment ("\#") or a simple
728      "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol
729      specifies a "must be used with" or a "must not be used with"
730      relationship, respectively.  If no rule is specified, then it is
731      assumed that the two packages are compatible and will function
732      either with or without each other.
733      
734    \item[--pdefault='PKG1 PKG2 PKG3 ...'] specifies the default set of
735      packages to be used.
736      
737      If not set, the default package list will be read from {\em
738        pkg/pkg\_default}
739      
740    \item[--adof=/path/to/file] specifies the "adjoint" or automatic
741      differentiation options file to be used.  The file is analogous to
742      the ``optfile'' defined above but it specifies information for the
743      AD build process.
744      
745      The default file is located in {\em
746        tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
747      and "TAMC" compilers.  An alternate version is also available at
748      {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
749      "STAF" compiler.  As with any compilers, it is helpful to have their
750      directories listed in your {\tt \$PATH} environment variable.
751      
752    \item[--mods='DIR1 DIR2 DIR3 ...'] specifies a list of directories
753      containing ``modifications''.  These directories contain files with
754      names that may (or may not) exist in the main MITgcm source tree but
755      will be overridden by any identically-named sources within the
756      ``MODS'' directories.
757      
758      The order of precedence for this "name-hiding" is as follows:
759      \begin{itemize}
760      \item ``MODS'' directories (in the order given)
761      \item Packages either explicitly specified or provided by default
762        (in the order given)
763      \item Packages included due to package dependencies (in the order
764        that that package dependencies are parsed)
765      \item The "standard dirs" (which may have been specified by the
766        ``-standarddirs'' option)
767      \end{itemize}
768      
769    \item[--make=/path/to/gmake] Due to the poor handling of soft-links and
770      other bugs common with the \texttt{make} versions provided by
771      commercial Unix vendors, GNU \texttt{make} (sometimes called
772      \texttt{gmake}) should be preferred.  This option provides a means
773      for specifying the make executable to be used.
774    
775    \end{description}
776    
777    
778    
779    \section{Running the model}
780    \label{sect:runModel}
781    
782    If compilation finished succesfuully (section \ref{sect:buildModel})
783    then an executable called {\em mitgcmuv} will now exist in the local
784    directory.
785    
786    To run the model as a single process (ie. not in parallel) simply
787    type:
788    \begin{verbatim}
789    % ./mitgcmuv
790    \end{verbatim}
791    The ``./'' is a safe-guard to make sure you use the local executable
792    in case you have others that exist in your path (surely odd if you
793    do!). The above command will spew out many lines of text output to
794    your screen.  This output contains details such as parameter values as
795    well as diagnostics such as mean Kinetic energy, largest CFL number,
796    etc. It is worth keeping this text output with the binary output so we
797    normally re-direct the {\em stdout} stream as follows:
798    \begin{verbatim}
799    % ./mitgcmuv > output.txt
800    \end{verbatim}
801    
802    For the example experiments in {\em vericication}, an example of the
803    output is kept in {\em results/output.txt} for comparison. You can compare
804    your {\em output.txt} with this one to check that the set-up works.
805    
806    
807    
808    \subsection{Output files}
809    
810  The model produces various output files. At a minimum, the instantaneous  The model produces various output files. At a minimum, the instantaneous
811  ``state'' of the model is written out, which is made of the following files:  ``state'' of the model is written out, which is made of the following files:
# Line 450  as the pickup files but are named differ Line 856  as the pickup files but are named differ
856  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
857  output to save disk space during long integrations.  output to save disk space during long integrations.
858    
859  \subsubsection{Looking at the output}  \subsection{Looking at the output}
860    
861  All the model data are written according to a ``meta/data'' file format.  All the model data are written according to a ``meta/data'' file format.
862  Each variable is associated with two files with suffix names \textit{.data}  Each variable is associated with two files with suffix names \textit{.data}
# Line 464  written in this format. The matlab scrip Line 870  written in this format. The matlab scrip
870  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads
871  the data. Look at the comments inside the script to see how to use it.  the data. Look at the comments inside the script to see how to use it.
872    
873  \section{Code structure}  Some examples of reading and visualizing some output in {\em Matlab}:
874    \begin{verbatim}
875    % matlab
876    >> H=rdmds('Depth');
877    >> contourf(H');colorbar;
878    >> title('Depth of fluid as used by model');
879    
880    >> eta=rdmds('Eta',10);
881    >> imagesc(eta');axis ij;colorbar;
882    >> title('Surface height at iter=10');
883    
884  \section{Doing it yourself: customizing the code}  >> eta=rdmds('Eta',[0:10:100]);
885    >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
886    \end{verbatim}
887    
888  \subsection{\protect\bigskip Configuration and setup}  \section{Doing it yourself: customizing the code}
889    
890  When you are ready to run the model in the configuration you want, the  When you are ready to run the model in the configuration you want, the
891  easiest thing is to use and adapt the setup of the case studies experiment  easiest thing is to use and adapt the setup of the case studies experiment
# Line 478  relative to the ''numerical model'' part Line 895  relative to the ''numerical model'' part
895  the ''execution environment'' part is covered in the parallel implementation  the ''execution environment'' part is covered in the parallel implementation
896  section) and on the variables and parameters that you are likely to change.  section) and on the variables and parameters that you are likely to change.
897    
898    \subsection{Configuration and setup}
899    
900  The CPP keys relative to the ''numerical model'' part of the code are all  The CPP keys relative to the ''numerical model'' part of the code are all
901  defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{%  defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{%
902  model/inc }or in one of the \textit{code }directories of the case study  model/inc }or in one of the \textit{code }directories of the case study
# Line 494  In what follows the parameters are group Line 913  In what follows the parameters are group
913  computational domain, the equations solved in the model, and the simulation  computational domain, the equations solved in the model, and the simulation
914  controls.  controls.
915    
916  \subsubsection{Computational domain, geometry and time-discretization}  \subsection{Computational domain, geometry and time-discretization}
917    
918  \begin{itemize}  \begin{itemize}
919  \item dimensions  \item dimensions
# Line 577  here I think. To come soon...) Line 996  here I think. To come soon...)
996  \item time-discretization  \item time-discretization
997  \end{itemize}  \end{itemize}
998    
999  The time steps are set through the real variables \textbf{deltaTMom }and  The time steps are set through the real variables \textbf{deltaTMom}
1000  \textbf{deltaTtracer }(in s) which represent the time step for the momentum  and \textbf{deltaTtracer} (in s) which represent the time step for the
1001  and tracer equations, respectively. For synchronous integrations, simply set  momentum and tracer equations, respectively. For synchronous
1002  the two variables to the same value (or you can prescribe one time step only  integrations, simply set the two variables to the same value (or you
1003  through the variable \textbf{deltaT}). The Adams-Bashforth stabilizing  can prescribe one time step only through the variable
1004  parameter is set through the variable \textbf{abEps }(dimensionless). The  \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
1005  stagger baroclinic time stepping can be activated by setting the logical  through the variable \textbf{abEps} (dimensionless). The stagger
1006  variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'.  baroclinic time stepping can be activated by setting the logical
1007    variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
1008  \subsubsection{Equation of state}  
1009    \subsection{Equation of state}
1010  First, because the model equations are written in terms of perturbations, a  
1011  reference thermodynamic state needs to be specified. This is done through  First, because the model equations are written in terms of
1012  the 1D arrays \textbf{tRef}\textit{\ }and \textbf{sRef}. \textbf{tRef }%  perturbations, a reference thermodynamic state needs to be specified.
1013  specifies the reference potential temperature profile (in $^{o}$C for  This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}.
1014  the ocean and $^{o}$K for the atmosphere) starting from the level  \textbf{tRef} specifies the reference potential temperature profile
1015  k=1. Similarly, \textbf{sRef}\textit{\ }specifies the reference salinity  (in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting
1016  profile (in ppt) for the ocean or the reference specific humidity profile  from the level k=1. Similarly, \textbf{sRef} specifies the reference
1017  (in g/kg) for the atmosphere.  salinity profile (in ppt) for the ocean or the reference specific
1018    humidity profile (in g/kg) for the atmosphere.
1019  The form of the equation of state is controlled by the character variables  
1020  \textbf{buoyancyRelation}\textit{\ }and \textbf{eosType}\textit{. }\textbf{%  The form of the equation of state is controlled by the character
1021  buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and  variables \textbf{buoyancyRelation} and \textbf{eosType}.
1022  needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In  \textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and
1023  this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'.  needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations.
1024  For the ocean, two forms of the equation of state are available: linear (set  In this case, \textbf{eosType} must be set to '\texttt{IDEALGAS}'.
1025  \textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial  For the ocean, two forms of the equation of state are available:
1026  approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\  linear (set \textbf{eosType} to '\texttt{LINEAR}') and a polynomial
1027  }to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the  approximation to the full nonlinear equation ( set
1028  thermal and haline expansion coefficients represented by the variables  \textbf{eosType}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear
1029  \textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(in ppt$%  case, you need to specify the thermal and haline expansion
1030  ^{-1}$). For the nonlinear case, you need to generate a file of polynomial  coefficients represented by the variables \textbf{tAlpha}\textit{\
1031  coefficients called \textit{POLY3.COEFFS. }To do this, use the program    }(in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For the nonlinear
1032  \textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is  case, you need to generate a file of polynomial coefficients called
1033  available in the same directory and you will need to edit the number and the  \textit{POLY3.COEFFS}. To do this, use the program
1034  values of the vertical levels in \textit{knudsen2.f }so that they match  \textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is
1035  those of your configuration). \textit{\ }  available in the same directory and you will need to edit the number
1036    and the values of the vertical levels in \textit{knudsen2.f} so that
1037    they match those of your configuration).
1038    
1039    There there are also higher polynomials for the equation of state:
1040    \begin{description}
1041    \item['\texttt{UNESCO}':] The UNESCO equation of state formula of
1042      Fofonoff and Millard \cite{fofonoff83}. This equation of state
1043      assumes in-situ temperature, which is not a model variable; \emph{its use
1044      is therefore discouraged, and it is only listed for completeness}.
1045    \item['\texttt{JMD95Z}':] A modified UNESCO formula by Jackett and
1046      McDougall \cite{jackett95}, which uses the model variable potential
1047      temperature as input. The '\texttt{Z}' indicates that this equation
1048      of state uses a horizontally and temporally constant pressure
1049      $p_{0}=-g\rho_{0}z$.
1050    \item['\texttt{JMD95P}':] A modified UNESCO formula by Jackett and
1051      McDougall \cite{jackett95}, which uses the model variable potential
1052      temperature as input. The '\texttt{P}' indicates that this equation
1053      of state uses the actual hydrostatic pressure of the last time
1054      step. Lagging the pressure in this way requires an additional pickup
1055      file for restarts.
1056    \item['\texttt{MDJWF}':] The new, more accurate and less expensive
1057      equation of state by McDougall et~al. \cite{mcdougall03}. It also
1058      requires lagging the pressure and therefore an additional pickup
1059      file for restarts.
1060    \end{description}
1061    For none of these options an reference profile of temperature or
1062    salinity is required.
1063    
1064  \subsubsection{Momentum equations}  \subsection{Momentum equations}
1065    
1066  In this section, we only focus for now on the parameters that you are likely  In this section, we only focus for now on the parameters that you are likely
1067  to change, i.e. the ones relative to forcing and dissipation for example.  to change, i.e. the ones relative to forcing and dissipation for example.
# Line 719  geopotential (for the atmosphere) you ne Line 1165  geopotential (for the atmosphere) you ne
1165  \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you  \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you
1166  want to deal with the ocean upper or atmosphere lower boundary).  want to deal with the ocean upper or atmosphere lower boundary).
1167    
1168  \subsubsection{Tracer equations}  \subsection{Tracer equations}
1169    
1170  This section covers the tracer equations i.e. the potential temperature  This section covers the tracer equations i.e. the potential temperature
1171  equation and the salinity (for the ocean) or specific humidity (for the  equation and the salinity (for the ocean) or specific humidity (for the
# Line 810  wish the tracer vertical diffusivities t Line 1256  wish the tracer vertical diffusivities t
1256  vertically due to static instabilities. Note that \textbf{cadjFreq }and  vertically due to static instabilities. Note that \textbf{cadjFreq }and
1257  \textbf{ivdc\_kappa }can not both have non-zero value.  \textbf{ivdc\_kappa }can not both have non-zero value.
1258    
1259  \subsubsection{Simulation controls}  \subsection{Simulation controls}
1260    
1261  The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s)  The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s)
1262  which determines the IO frequencies and is used in tagging output.  which determines the IO frequencies and is used in tagging output.
# Line 846  fields can be written out by setting the Line 1292  fields can be written out by setting the
1292  The precision with which to write the binary data is controlled by the  The precision with which to write the binary data is controlled by the
1293  integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%  integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%
1294  64}).  64}).
1295    
1296    %%% Local Variables:
1297    %%% mode: latex
1298    %%% TeX-master: t
1299    %%% End:
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