17 |
|
|
18 |
\section{Where to find information} |
\section{Where to find information} |
19 |
\label{sect:whereToFindInfo} |
\label{sect:whereToFindInfo} |
20 |
|
\begin{rawhtml} |
21 |
|
<!-- CMIREDIR:whereToFindInfo: --> |
22 |
|
\end{rawhtml} |
23 |
|
|
24 |
A web site is maintained for release 1 (Sealion) of MITgcm: |
A web site is maintained for release 2 (``Pelican'') of MITgcm: |
25 |
|
\begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml} |
26 |
\begin{verbatim} |
\begin{verbatim} |
27 |
http://mitgcm.org/sealion |
http://mitgcm.org/pelican |
28 |
\end{verbatim} |
\end{verbatim} |
29 |
|
\begin{rawhtml} </A> \end{rawhtml} |
30 |
Here you will find an on-line version of this document, a |
Here you will find an on-line version of this document, a |
31 |
``browsable'' copy of the code and a searchable database of the model |
``browsable'' copy of the code and a searchable database of the model |
32 |
and site, as well as links for downloading the model and |
and site, as well as links for downloading the model and |
33 |
documentation, to data-sources and other related sites. |
documentation, to data-sources, and other related sites. |
34 |
|
|
35 |
There is also a support news group for the model that you can email at |
There is also a web-archived support mailing list for the model that |
36 |
\texttt{support@mitgcm.org} or browse at: |
you can email at \texttt{MITgcm-support@mitgcm.org} or browse at: |
37 |
|
\begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml} |
38 |
\begin{verbatim} |
\begin{verbatim} |
39 |
news://mitgcm.org/mitgcm.support |
http://mitgcm.org/mailman/listinfo/mitgcm-support/ |
40 |
|
http://mitgcm.org/pipermail/mitgcm-support/ |
41 |
\end{verbatim} |
\end{verbatim} |
42 |
A mail to the email list will reach all the developers and be archived |
\begin{rawhtml} </A> \end{rawhtml} |
43 |
on the newsgroup. A users email list will be established at some time |
Essentially all of the MITgcm web pages can be searched using a |
44 |
in the future. |
popular web crawler such as Google or through our own search facility: |
45 |
|
\begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml} |
46 |
|
\begin{verbatim} |
47 |
|
http://mitgcm.org/htdig/ |
48 |
|
\end{verbatim} |
49 |
|
\begin{rawhtml} </A> \end{rawhtml} |
50 |
|
%%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org |
51 |
|
|
52 |
|
|
53 |
|
|
54 |
\section{Obtaining the code} |
\section{Obtaining the code} |
55 |
\label{sect:obtainingCode} |
\label{sect:obtainingCode} |
56 |
|
\begin{rawhtml} |
57 |
|
<!-- CMIREDIR:obtainingCode: --> |
58 |
|
\end{rawhtml} |
59 |
|
|
60 |
|
MITgcm can be downloaded from our system by following |
61 |
|
the instructions below. As a courtesy we ask that you send e-mail to us at |
62 |
|
\begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml} |
63 |
|
MITgcm-support@mitgcm.org |
64 |
|
\begin{rawhtml} </A> \end{rawhtml} |
65 |
|
to enable us to keep track of who's using the model and in what application. |
66 |
|
You can download the model two ways: |
67 |
|
|
68 |
|
\begin{enumerate} |
69 |
|
\item Using CVS software. CVS is a freely available source code management |
70 |
|
tool. To use CVS you need to have the software installed. Many systems |
71 |
|
come with CVS pre-installed, otherwise good places to look for |
72 |
|
the software for a particular platform are |
73 |
|
\begin{rawhtml} <A href=http://www.cvshome.org/ target="idontexist"> \end{rawhtml} |
74 |
|
cvshome.org |
75 |
|
\begin{rawhtml} </A> \end{rawhtml} |
76 |
|
and |
77 |
|
\begin{rawhtml} <A href=http://www.wincvs.org/ target="idontexist"> \end{rawhtml} |
78 |
|
wincvs.org |
79 |
|
\begin{rawhtml} </A> \end{rawhtml} |
80 |
|
. |
81 |
|
|
82 |
|
\item Using a tar file. This method is simple and does not |
83 |
|
require any special software. However, this method does not |
84 |
|
provide easy support for maintenance updates. |
85 |
|
|
86 |
|
\end{enumerate} |
87 |
|
|
88 |
|
\subsection{Method 1 - Checkout from CVS} |
89 |
|
\label{sect:cvs_checkout} |
90 |
|
|
91 |
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 |
92 |
provides an efficient and elegant way of organizing your code and keeping |
provides an efficient and elegant way of organizing your code and keeping |
93 |
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 |
94 |
download a tar file. |
download a tar file. |
95 |
|
|
96 |
Before you can use CVS, the following environment variable has to be set in |
Before you can use CVS, the following environment variable(s) should |
97 |
your .cshrc or .tcshrc: |
be set within your shell. For a csh or tcsh shell, put the following |
98 |
\begin{verbatim} |
\begin{verbatim} |
99 |
% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack |
% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack |
|
% cvs login ( CVS password: cvsanon ) |
|
100 |
\end{verbatim} |
\end{verbatim} |
101 |
|
in your \texttt{.cshrc} or \texttt{.tcshrc} file. For bash or sh |
102 |
|
shells, put: |
103 |
|
\begin{verbatim} |
104 |
|
% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
105 |
|
\end{verbatim} |
106 |
|
in your \texttt{.profile} or \texttt{.bashrc} file. |
107 |
|
|
108 |
|
|
109 |
You only need to do ``cvs login'' once. To obtain the source for the release: |
To get MITgcm through CVS, first register with the MITgcm CVS server |
110 |
|
using command: |
111 |
\begin{verbatim} |
\begin{verbatim} |
112 |
% cvs co -d directory -P -r release1 MITgcmUV |
% cvs login ( CVS password: cvsanon ) |
113 |
\end{verbatim} |
\end{verbatim} |
114 |
|
You only need to do a ``cvs login'' once. |
115 |
|
|
116 |
This creates a directory called \textit{directory}. If \textit{directory} |
To obtain the latest sources type: |
|
exists this command updates your code based on the repository. Each |
|
|
directory in the source tree contains a directory \textit{CVS}. This |
|
|
information is required by CVS to keep track of your file versions with |
|
|
respect to the repository. Don't edit the files in \textit{CVS}! To obtain a |
|
|
different \textit{version} that is not the latest source: |
|
117 |
\begin{verbatim} |
\begin{verbatim} |
118 |
% cvs co -d directory -P -r version MITgcm |
% cvs co MITgcm |
119 |
\end{verbatim} |
\end{verbatim} |
120 |
or the latest development version: |
or to get a specific release type: |
121 |
|
\begin{verbatim} |
122 |
|
% cvs co -P -r checkpoint52i_post MITgcm |
123 |
|
\end{verbatim} |
124 |
|
The MITgcm web site contains further directions concerning the source |
125 |
|
code and CVS. It also contains a web interface to our CVS archive so |
126 |
|
that one may easily view the state of files, revisions, and other |
127 |
|
development milestones: |
128 |
|
\begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml} |
129 |
|
\begin{verbatim} |
130 |
|
http://mitgcm.org/source_code.html |
131 |
|
\end{verbatim} |
132 |
|
\begin{rawhtml} </A> \end{rawhtml} |
133 |
|
|
134 |
|
As a convenience, the MITgcm CVS server contains aliases which are |
135 |
|
named subsets of the codebase. These aliases can be especially |
136 |
|
helpful when used over slow internet connections or on machines with |
137 |
|
restricted storage space. Table \ref{tab:cvsModules} contains a list |
138 |
|
of CVS aliases |
139 |
|
\begin{table}[htb] |
140 |
|
\centering |
141 |
|
\begin{tabular}[htb]{|lp{3.25in}|}\hline |
142 |
|
\textbf{Alias Name} & \textbf{Information (directories) Contained} \\\hline |
143 |
|
\texttt{MITgcm\_code} & Only the source code -- none of the verification examples. \\ |
144 |
|
\texttt{MITgcm\_verif\_basic} |
145 |
|
& Source code plus a small set of the verification examples |
146 |
|
(\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5}, |
147 |
|
\texttt{front\_relax}, and \texttt{plume\_on\_slope}). \\ |
148 |
|
\texttt{MITgcm\_verif\_atmos} & Source code plus all of the atmospheric examples. \\ |
149 |
|
\texttt{MITgcm\_verif\_ocean} & Source code plus all of the oceanic examples. \\ |
150 |
|
\texttt{MITgcm\_verif\_all} & Source code plus all of the |
151 |
|
verification examples. \\\hline |
152 |
|
\end{tabular} |
153 |
|
\caption{MITgcm CVS Modules} |
154 |
|
\label{tab:cvsModules} |
155 |
|
\end{table} |
156 |
|
|
157 |
|
The checkout process creates a directory called \texttt{MITgcm}. If |
158 |
|
the directory \texttt{MITgcm} exists this command updates your code |
159 |
|
based on the repository. Each directory in the source tree contains a |
160 |
|
directory \texttt{CVS}. This information is required by CVS to keep |
161 |
|
track of your file versions with respect to the repository. Don't edit |
162 |
|
the files in \texttt{CVS}! You can also use CVS to download code |
163 |
|
updates. More extensive information on using CVS for maintaining |
164 |
|
MITgcm code can be found |
165 |
|
\begin{rawhtml} <A href="http://mitgcm.org/usingcvstoget.html" target="idontexist"> \end{rawhtml} |
166 |
|
here |
167 |
|
\begin{rawhtml} </A> \end{rawhtml} |
168 |
|
. |
169 |
|
It is important to note that the CVS aliases in Table |
170 |
|
\ref{tab:cvsModules} cannot be used in conjunction with the CVS |
171 |
|
\texttt{-d DIRNAME} option. However, the \texttt{MITgcm} directories |
172 |
|
they create can be changed to a different name following the check-out: |
173 |
\begin{verbatim} |
\begin{verbatim} |
174 |
% cvs co -d directory -P MITgcm |
% cvs co MITgcm_verif_basic |
175 |
|
% mv MITgcm MITgcm_verif_basic |
176 |
\end{verbatim} |
\end{verbatim} |
177 |
|
|
178 |
\paragraph*{Conventional download method} |
|
179 |
|
\subsection{Method 2 - Tar file download} |
180 |
\label{sect:conventionalDownload} |
\label{sect:conventionalDownload} |
181 |
|
|
182 |
If you do not have CVS on your system, you can download the model as a |
If you do not have CVS on your system, you can download the model as a |
183 |
tar file from the reference web site at: |
tar file from the web site at: |
184 |
|
\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml} |
185 |
\begin{verbatim} |
\begin{verbatim} |
186 |
http://mitgcm.org/download/ |
http://mitgcm.org/download/ |
187 |
\end{verbatim} |
\end{verbatim} |
188 |
|
\begin{rawhtml} </A> \end{rawhtml} |
189 |
The tar file still contains CVS information which we urge you not to |
The tar file still contains CVS information which we urge you not to |
190 |
delete; even if you do not use CVS yourself the information can help |
delete; even if you do not use CVS yourself the information can help |
191 |
us if you should need to send us your copy of the code. |
us if you should need to send us your copy of the code. If a recent |
192 |
|
tar file does not exist, then please contact the developers through |
193 |
|
the |
194 |
|
\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
195 |
|
MITgcm-support@mitgcm.org |
196 |
|
\begin{rawhtml} </A> \end{rawhtml} |
197 |
|
mailing list. |
198 |
|
|
199 |
|
\subsubsection{Upgrading from an earlier version} |
200 |
|
|
201 |
|
If you already have an earlier version of the code you can ``upgrade'' |
202 |
|
your copy instead of downloading the entire repository again. First, |
203 |
|
``cd'' (change directory) to the top of your working copy: |
204 |
|
\begin{verbatim} |
205 |
|
% cd MITgcm |
206 |
|
\end{verbatim} |
207 |
|
and then issue the cvs update command such as: |
208 |
|
\begin{verbatim} |
209 |
|
% cvs -q update -r checkpoint52i_post -d -P |
210 |
|
\end{verbatim} |
211 |
|
This will update the ``tag'' to ``checkpoint52i\_post'', add any new |
212 |
|
directories (-d) and remove any empty directories (-P). The -q option |
213 |
|
means be quiet which will reduce the number of messages you'll see in |
214 |
|
the terminal. If you have modified the code prior to upgrading, CVS |
215 |
|
will try to merge your changes with the upgrades. If there is a |
216 |
|
conflict between your modifications and the upgrade, it will report |
217 |
|
that file with a ``C'' in front, e.g.: |
218 |
|
\begin{verbatim} |
219 |
|
C model/src/ini_parms.F |
220 |
|
\end{verbatim} |
221 |
|
If the list of conflicts scrolled off the screen, you can re-issue the |
222 |
|
cvs update command and it will report the conflicts. Conflicts are |
223 |
|
indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and |
224 |
|
``$>>>>>>>$''. For example, |
225 |
|
{\small |
226 |
|
\begin{verbatim} |
227 |
|
<<<<<<< ini_parms.F |
228 |
|
& bottomDragLinear,myOwnBottomDragCoefficient, |
229 |
|
======= |
230 |
|
& bottomDragLinear,bottomDragQuadratic, |
231 |
|
>>>>>>> 1.18 |
232 |
|
\end{verbatim} |
233 |
|
} |
234 |
|
means that you added ``myOwnBottomDragCoefficient'' to a namelist at |
235 |
|
the same time and place that we added ``bottomDragQuadratic''. You |
236 |
|
need to resolve this conflict and in this case the line should be |
237 |
|
changed to: |
238 |
|
{\small |
239 |
|
\begin{verbatim} |
240 |
|
& bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient, |
241 |
|
\end{verbatim} |
242 |
|
} |
243 |
|
and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted. |
244 |
|
Unless you are making modifications which exactly parallel |
245 |
|
developments we make, these types of conflicts should be rare. |
246 |
|
|
247 |
|
\paragraph*{Upgrading to the current pre-release version} |
248 |
|
|
249 |
|
We don't make a ``release'' for every little patch and bug fix in |
250 |
|
order to keep the frequency of upgrades to a minimum. However, if you |
251 |
|
have run into a problem for which ``we have already fixed in the |
252 |
|
latest code'' and we haven't made a ``tag'' or ``release'' since that |
253 |
|
patch then you'll need to get the latest code: |
254 |
|
\begin{verbatim} |
255 |
|
% cvs -q update -A -d -P |
256 |
|
\end{verbatim} |
257 |
|
Unlike, the ``check-out'' and ``update'' procedures above, there is no |
258 |
|
``tag'' or release name. The -A tells CVS to upgrade to the |
259 |
|
very latest version. As a rule, we don't recommend this since you |
260 |
|
might upgrade while we are in the processes of checking in the code so |
261 |
|
that you may only have part of a patch. Using this method of updating |
262 |
|
also means we can't tell what version of the code you are working |
263 |
|
with. So please be sure you understand what you're doing. |
264 |
|
|
265 |
\section{Model and directory structure} |
\section{Model and directory structure} |
266 |
|
\begin{rawhtml} |
267 |
|
<!-- CMIREDIR:directory_structure: --> |
268 |
|
\end{rawhtml} |
269 |
|
|
270 |
|
The ``numerical'' model is contained within a execution environment |
271 |
|
support wrapper. This wrapper is designed to provide a general |
272 |
|
framework for grid-point models. MITgcmUV is a specific numerical |
273 |
|
model that uses the framework. Under this structure the model is split |
274 |
|
into execution environment support code and conventional numerical |
275 |
|
model code. The execution environment support code is held under the |
276 |
|
\texttt{eesupp} directory. The grid point model code is held under the |
277 |
|
\texttt{model} directory. Code execution actually starts in the |
278 |
|
\texttt{eesupp} routines and not in the \texttt{model} routines. For |
279 |
|
this reason the top-level \texttt{MAIN.F} is in the |
280 |
|
\texttt{eesupp/src} directory. In general, end-users should not need |
281 |
|
to worry about this level. The top-level routine for the numerical |
282 |
|
part of the code is in \texttt{model/src/THE\_MODEL\_MAIN.F}. Here is |
283 |
|
a brief description of the directory structure of the model under the |
284 |
|
root tree (a detailed description is given in section 3: Code |
285 |
|
structure). |
286 |
|
|
287 |
|
\begin{itemize} |
288 |
|
|
289 |
|
\item \texttt{bin}: this directory is initially empty. It is the |
290 |
|
default directory in which to compile the code. |
291 |
|
|
292 |
|
\item \texttt{diags}: contains the code relative to time-averaged |
293 |
|
diagnostics. It is subdivided into two subdirectories \texttt{inc} |
294 |
|
and \texttt{src} that contain include files (\texttt{*.h} files) and |
295 |
|
Fortran subroutines (\texttt{*.F} files), respectively. |
296 |
|
|
297 |
|
\item \texttt{doc}: contains brief documentation notes. |
298 |
|
|
299 |
|
\item \texttt{eesupp}: contains the execution environment source code. |
300 |
|
Also subdivided into two subdirectories \texttt{inc} and |
301 |
|
\texttt{src}. |
302 |
|
|
303 |
|
\item \texttt{exe}: this directory is initially empty. It is the |
304 |
|
default directory in which to execute the code. |
305 |
|
|
306 |
|
\item \texttt{model}: this directory contains the main source code. |
307 |
|
Also subdivided into two subdirectories \texttt{inc} and |
308 |
|
\texttt{src}. |
309 |
|
|
310 |
|
\item \texttt{pkg}: contains the source code for the packages. Each |
311 |
|
package corresponds to a subdirectory. For example, \texttt{gmredi} |
312 |
|
contains the code related to the Gent-McWilliams/Redi scheme, |
313 |
|
\texttt{aim} the code relative to the atmospheric intermediate |
314 |
|
physics. The packages are described in detail in section 3. |
315 |
|
|
316 |
|
\item \texttt{tools}: this directory contains various useful tools. |
317 |
|
For example, \texttt{genmake2} is a script written in csh (C-shell) |
318 |
|
that should be used to generate your makefile. The directory |
319 |
|
\texttt{adjoint} contains the makefile specific to the Tangent |
320 |
|
linear and Adjoint Compiler (TAMC) that generates the adjoint code. |
321 |
|
The latter is described in details in part V. |
322 |
|
|
323 |
|
\item \texttt{utils}: this directory contains various utilities. The |
324 |
|
subdirectory \texttt{knudsen2} contains code and a makefile that |
325 |
|
compute coefficients of the polynomial approximation to the knudsen |
326 |
|
formula for an ocean nonlinear equation of state. The |
327 |
|
\texttt{matlab} subdirectory contains matlab scripts for reading |
328 |
|
model output directly into matlab. \texttt{scripts} contains C-shell |
329 |
|
post-processing scripts for joining processor-based and tiled-based |
330 |
|
model output. |
331 |
|
|
332 |
|
\item \texttt{verification}: this directory contains the model |
333 |
|
examples. See section \ref{sect:modelExamples}. |
334 |
|
|
|
The ``numerical'' model is contained within a execution environment support |
|
|
wrapper. This wrapper is designed to provide a general framework for |
|
|
grid-point models. MITgcmUV is a specific numerical model that uses the |
|
|
framework. Under this structure the model is split into execution |
|
|
environment support code and conventional numerical model code. The |
|
|
execution environment support code is held under the \textit{eesupp} |
|
|
directory. The grid point model code is held under the \textit{model} |
|
|
directory. Code execution actually starts in the \textit{eesupp} routines |
|
|
and not in the \textit{model} routines. For this reason the top-level |
|
|
\textit{MAIN.F} is in the \textit{eesupp/src} directory. In general, |
|
|
end-users should not need to worry about this level. The top-level routine |
|
|
for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F% |
|
|
}. Here is a brief description of the directory structure of the model under |
|
|
the root tree (a detailed description is given in section 3: Code structure). |
|
|
|
|
|
\begin{itemize} |
|
|
\item \textit{bin}: this directory is initially empty. It is the default |
|
|
directory in which to compile the code. |
|
|
|
|
|
\item \textit{diags}: contains the code relative to time-averaged |
|
|
diagnostics. It is subdivided into two subdirectories \textit{inc} and |
|
|
\textit{src} that contain include files (*.\textit{h} files) and fortran |
|
|
subroutines (*.\textit{F} files), respectively. |
|
|
|
|
|
\item \textit{doc}: contains brief documentation notes. |
|
|
|
|
|
\item \textit{eesupp}: contains the execution environment source code. Also |
|
|
subdivided into two subdirectories \textit{inc} and \textit{src}. |
|
|
|
|
|
\item \textit{exe}: this directory is initially empty. It is the default |
|
|
directory in which to execute the code. |
|
|
|
|
|
\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} contains the |
|
|
code related to the Gent-McWilliams/Redi scheme, \textit{aim} the code |
|
|
relative to the atmospheric intermediate physics. The packages are described |
|
|
in detail in section 3. |
|
|
|
|
|
\item \textit{tools}: this directory contains various useful tools. For |
|
|
example, \textit{genmake} is a script written in csh (C-shell) that should |
|
|
be used to generate your makefile. The directory \textit{adjoint} contains |
|
|
the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that |
|
|
generates the adjoint code. The latter is described in details in part V. |
|
|
|
|
|
\item \textit{utils}: this directory contains various utilities. The |
|
|
subdirectory \textit{knudsen2} contains code and a makefile that |
|
|
compute coefficients of the polynomial approximation to the knudsen |
|
|
formula for an ocean nonlinear equation of state. The \textit{matlab} |
|
|
subdirectory contains matlab scripts for reading model output directly |
|
|
into matlab. \textit{scripts} contains C-shell post-processing |
|
|
scripts for joining processor-based and tiled-based model output. |
|
|
|
|
|
\item \textit{verification}: this directory contains the model examples. See |
|
|
section \ref{sect:modelExamples}. |
|
|
\end{itemize} |
|
|
|
|
|
\section{Example experiments} |
|
|
\label{sect:modelExamples} |
|
|
|
|
|
Now that you have successfully downloaded the model code we recommend that |
|
|
you first try to run the examples provided with the base version. You will |
|
|
probably want to run the example that is the closest to the configuration |
|
|
you will use eventually. The examples are located in subdirectories under |
|
|
the directory \textit{verification} and are briefly described below (a full |
|
|
description is given in section 2): |
|
|
|
|
|
\subsection{List of model examples} |
|
|
|
|
|
\begin{itemize} |
|
|
\item \textit{exp0} - single layer, ocean double gyre (barotropic with |
|
|
free-surface). |
|
|
|
|
|
\item \textit{exp1} - 4 layers, ocean double gyre. |
|
|
|
|
|
\item \textit{exp2} - 4x4 degree global ocean simulation with steady |
|
|
climatological forcing. |
|
|
|
|
|
\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, 5 layers |
|
|
Molteni physics package. Global Zonal Mean configuration, 1x64x5 resolution. |
|
|
|
|
|
\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric |
|
|
physics, 5 layers Molteni physics package. Equatorial Slice configuration. |
|
|
2D (X-Z). |
|
|
|
|
|
\item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric |
|
|
physics, 5 layers Molteni physics package. 3D Equatorial Channel |
|
|
configuration (not completely tested). |
|
|
|
|
|
\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers |
|
|
Molteni physics package. Global configuration, 128x64x5 resolution. |
|
|
|
|
|
\item \textit{adjustment.128x64x1} |
|
|
|
|
|
\item \textit{adjustment.cs-32x32x1} |
|
335 |
\end{itemize} |
\end{itemize} |
336 |
|
|
337 |
\subsection{Directory structure of model examples} |
\section[Building MITgcm]{Building the code} |
|
|
|
|
Each example directory has the following subdirectories: |
|
|
|
|
|
\begin{itemize} |
|
|
\item \textit{code}: contains the code particular to the example. At a |
|
|
minimum, this directory includes the following files: |
|
|
|
|
|
\begin{itemize} |
|
|
\item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to the |
|
|
``execution environment'' part of the code. The default version is located |
|
|
in \textit{eesupp/inc}. |
|
|
|
|
|
\item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the |
|
|
``numerical model'' part of the code. The default version is located in |
|
|
\textit{model/inc}. |
|
|
|
|
|
\item \textit{code/SIZE.h}: declares size of underlying computational grid. |
|
|
The default version is located in \textit{model/inc}. |
|
|
\end{itemize} |
|
|
|
|
|
In addition, other include files and subroutines might be present in \textit{% |
|
|
code} depending on the particular experiment. See section 2 for more details. |
|
|
|
|
|
\item \textit{input}: contains the input data files required to run the |
|
|
example. At a mimimum, the \textit{input} directory contains the following |
|
|
files: |
|
|
|
|
|
\begin{itemize} |
|
|
\item \textit{input/data}: this file, written as a namelist, specifies the |
|
|
main parameters for the experiment. |
|
|
|
|
|
\item \textit{input/data.pkg}: contains parameters relative to the packages |
|
|
used in the experiment. |
|
|
|
|
|
\item \textit{input/eedata}: this file contains ``execution environment'' |
|
|
data. At present, this consists of a specification of the number of threads |
|
|
to use in $X$ and $Y$ under multithreaded execution. |
|
|
\end{itemize} |
|
|
|
|
|
In addition, you will also find in this directory the forcing and topography |
|
|
files as well as the files describing the initial state of the experiment. |
|
|
This varies from experiment to experiment. See section 2 for more details. |
|
|
|
|
|
\item \textit{results}: this directory contains the output file \textit{% |
|
|
output.txt} produced by the simulation example. This file is useful for |
|
|
comparison with your own output when you run the experiment. |
|
|
\end{itemize} |
|
|
|
|
|
Once you have chosen the example you want to run, you are ready to compile |
|
|
the code. |
|
|
|
|
|
\section{Building the code} |
|
338 |
\label{sect:buildingCode} |
\label{sect:buildingCode} |
339 |
|
\begin{rawhtml} |
340 |
|
<!-- CMIREDIR:buildingCode: --> |
341 |
|
\end{rawhtml} |
342 |
|
|
343 |
|
To compile the code, we use the \texttt{make} program. This uses a |
344 |
|
file (\texttt{Makefile}) that allows us to pre-process source files, |
345 |
|
specify compiler and optimization options and also figures out any |
346 |
|
file dependencies. We supply a script (\texttt{genmake2}), described |
347 |
|
in section \ref{sect:genmake}, that automatically creates the |
348 |
|
\texttt{Makefile} for you. You then need to build the dependencies and |
349 |
|
compile the code. |
350 |
|
|
351 |
|
As an example, assume that you want to build and run experiment |
352 |
|
\texttt{verification/exp2}. The are multiple ways and places to |
353 |
|
actually do this but here let's build the code in |
354 |
|
\texttt{verification/exp2/build}: |
355 |
|
\begin{verbatim} |
356 |
|
% cd verification/exp2/build |
357 |
|
\end{verbatim} |
358 |
|
First, build the \texttt{Makefile}: |
359 |
|
\begin{verbatim} |
360 |
|
% ../../../tools/genmake2 -mods=../code |
361 |
|
\end{verbatim} |
362 |
|
The command line option tells \texttt{genmake} to override model source |
363 |
|
code with any files in the directory \texttt{../code/}. |
364 |
|
|
365 |
|
On many systems, the \texttt{genmake2} program will be able to |
366 |
|
automatically recognize the hardware, find compilers and other tools |
367 |
|
within the user's path (``\texttt{echo \$PATH}''), and then choose an |
368 |
|
appropriate set of options from the files (``optfiles'') contained in |
369 |
|
the \texttt{tools/build\_options} directory. Under some |
370 |
|
circumstances, a user may have to create a new ``optfile'' in order to |
371 |
|
specify the exact combination of compiler, compiler flags, libraries, |
372 |
|
and other options necessary to build a particular configuration of |
373 |
|
MITgcm. In such cases, it is generally helpful to read the existing |
374 |
|
``optfiles'' and mimic their syntax. |
375 |
|
|
376 |
|
Through the MITgcm-support list, the MITgcm developers are willing to |
377 |
|
provide help writing or modifing ``optfiles''. And we encourage users |
378 |
|
to post new ``optfiles'' (particularly ones for new machines or |
379 |
|
architectures) to the |
380 |
|
\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
381 |
|
MITgcm-support@mitgcm.org |
382 |
|
\begin{rawhtml} </A> \end{rawhtml} |
383 |
|
list. |
384 |
|
|
385 |
To compile the code, we use the {\em make} program. This uses a file |
To specify an optfile to \texttt{genmake2}, the syntax is: |
|
({\em Makefile}) that allows us to pre-process source files, specify |
|
|
compiler and optimization options and also figures out any file |
|
|
dependancies. We supply a script ({\em genmake}), described in section |
|
|
\ref{sect:genmake}, that automatically creates the {\em Makefile} for |
|
|
you. You then need to build the dependancies and compile the code. |
|
|
|
|
|
As an example, let's assume that you want to build and run experiment |
|
|
\textit{verification/exp2}. The are multiple ways and places to actually |
|
|
do this but here let's build the code in |
|
|
\textit{verification/exp2/input}: |
|
|
\begin{verbatim} |
|
|
% cd verification/exp2/input |
|
|
\end{verbatim} |
|
|
First, build the {\em Makefile}: |
|
|
\begin{verbatim} |
|
|
% ../../../tools/genmake -mods=../code |
|
|
\end{verbatim} |
|
|
The command line option tells {\em genmake} to override model source |
|
|
code with any files in the directory {\em ./code/}. |
|
|
|
|
|
If there is no \textit{.genmakerc} in the \textit{input} directory, you have |
|
|
to use the following options when invoking \textit{genmake}: |
|
386 |
\begin{verbatim} |
\begin{verbatim} |
387 |
% ../../../tools/genmake -mods=../code |
% ../../../tools/genmake2 -mods=../code -of /path/to/optfile |
388 |
\end{verbatim} |
\end{verbatim} |
389 |
|
|
390 |
Next, create the dependancies: |
Once a \texttt{Makefile} has been generated, we create the |
391 |
|
dependencies with the command: |
392 |
\begin{verbatim} |
\begin{verbatim} |
393 |
% make depend |
% make depend |
394 |
\end{verbatim} |
\end{verbatim} |
395 |
This modifies {\em Makefile} by attaching a [long] list of files on |
This modifies the \texttt{Makefile} by attaching a (usually, long) |
396 |
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 |
397 |
re-compilation if and when you start to modify the code. {\tt make |
reduce re-compilation if and when you start to modify the code. The |
398 |
depend} also created links from the model source to this directory. |
{\tt make depend} command also creates links from the model source to |
399 |
|
this directory. It is important to note that the {\tt make depend} |
400 |
|
stage will occasionally produce warnings or errors since the |
401 |
|
dependency parsing tool is unable to find all of the necessary header |
402 |
|
files (\textit{eg.} \texttt{netcdf.inc}). In these circumstances, it |
403 |
|
is usually OK to ignore the warnings/errors and proceed to the next |
404 |
|
step. |
405 |
|
|
406 |
Now compile the code: |
Next one can compile the code using: |
407 |
\begin{verbatim} |
\begin{verbatim} |
408 |
% make |
% make |
409 |
\end{verbatim} |
\end{verbatim} |
410 |
The {\tt make} command creates an executable called \textit{mitgcmuv}. |
The {\tt make} command creates an executable called \texttt{mitgcmuv}. |
411 |
|
Additional make ``targets'' are defined within the makefile to aid in |
412 |
|
the production of adjoint and other versions of MITgcm. On SMP |
413 |
|
(shared multi-processor) systems, the build process can often be sped |
414 |
|
up appreciably using the command: |
415 |
|
\begin{verbatim} |
416 |
|
% make -j 2 |
417 |
|
\end{verbatim} |
418 |
|
where the ``2'' can be replaced with a number that corresponds to the |
419 |
|
number of CPUs available. |
420 |
|
|
421 |
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 |
422 |
given in section \ref{sect:runModel}. Here, we can run the model with: |
given in section \ref{sect:runModel}. Here, we can run the model by |
423 |
|
first creating links to all the input files: |
424 |
|
\begin{verbatim} |
425 |
|
ln -s ../input/* . |
426 |
|
\end{verbatim} |
427 |
|
and then calling the executable with: |
428 |
\begin{verbatim} |
\begin{verbatim} |
429 |
./mitgcmuv > output.txt |
./mitgcmuv > output.txt |
430 |
\end{verbatim} |
\end{verbatim} |
431 |
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 |
432 |
output.txt}. |
\texttt{output.txt}. |
|
|
|
433 |
|
|
434 |
\subsection{Building/compiling the code elsewhere} |
\subsection{Building/compiling the code elsewhere} |
435 |
|
|
438 |
convenience. You can also configure and compile the code in other |
convenience. You can also configure and compile the code in other |
439 |
locations, for example on a scratch disk with out having to copy the |
locations, for example on a scratch disk with out having to copy the |
440 |
entire source tree. The only requirement to do so is you have {\tt |
entire source tree. The only requirement to do so is you have {\tt |
441 |
genmake} in your path or you know the absolute path to {\tt genmake}. |
genmake2} in your path or you know the absolute path to {\tt |
442 |
|
genmake2}. |
443 |
|
|
444 |
The following sections outline some possible methods of organizing you |
The following sections outline some possible methods of organizing |
445 |
source and data. |
your source and data. |
446 |
|
|
447 |
\subsubsection{Building from the {\em ../code directory}} |
\subsubsection{Building from the {\em ../code directory}} |
448 |
|
|
449 |
This is just as simple as building in the {\em input/} directory: |
This is just as simple as building in the {\em input/} directory: |
450 |
\begin{verbatim} |
\begin{verbatim} |
451 |
% cd verification/exp2/code |
% cd verification/exp2/code |
452 |
% ../../../tools/genmake |
% ../../../tools/genmake2 |
453 |
% make depend |
% make depend |
454 |
% make |
% make |
455 |
\end{verbatim} |
\end{verbatim} |
460 |
% cp ../code/mitgcmuv ./ |
% cp ../code/mitgcmuv ./ |
461 |
% ./mitgcmuv > output.txt |
% ./mitgcmuv > output.txt |
462 |
\end{verbatim} |
\end{verbatim} |
463 |
or if you will be making muliple runs with the same executable: |
or if you will be making multiple runs with the same executable: |
464 |
\begin{verbatim} |
\begin{verbatim} |
465 |
% cd ../ |
% cd ../ |
466 |
% cp -r input run1 |
% cp -r input run1 |
472 |
\subsubsection{Building from a new directory} |
\subsubsection{Building from a new directory} |
473 |
|
|
474 |
Since the {\em input} directory contains input files it is often more |
Since the {\em input} directory contains input files it is often more |
475 |
useful to keep {\em input} prestine and build in a new directory |
useful to keep {\em input} pristine and build in a new directory |
476 |
within {\em verification/exp2/}: |
within {\em verification/exp2/}: |
477 |
\begin{verbatim} |
\begin{verbatim} |
478 |
% cd verification/exp2 |
% cd verification/exp2 |
479 |
% mkdir build |
% mkdir build |
480 |
% cd build |
% cd build |
481 |
% ../../../tools/genmake -mods=../code |
% ../../../tools/genmake2 -mods=../code |
482 |
% make depend |
% make depend |
483 |
% make |
% make |
484 |
\end{verbatim} |
\end{verbatim} |
500 |
% ./mitgcmuv > output.txt |
% ./mitgcmuv > output.txt |
501 |
\end{verbatim} |
\end{verbatim} |
502 |
|
|
503 |
\subsubsection{Building from on a scratch disk} |
\subsubsection{Building on a scratch disk} |
504 |
|
|
505 |
Model object files and output data can use up large amounts of disk |
Model object files and output data can use up large amounts of disk |
506 |
space so it is often the case that you will be operating on a large |
space so it is often the case that you will be operating on a large |
508 |
following commands will build the model in {\em /scratch/exp2-run1}: |
following commands will build the model in {\em /scratch/exp2-run1}: |
509 |
\begin{verbatim} |
\begin{verbatim} |
510 |
% cd /scratch/exp2-run1 |
% cd /scratch/exp2-run1 |
511 |
% ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code |
% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ |
512 |
|
-mods=~/MITgcm/verification/exp2/code |
513 |
% make depend |
% make depend |
514 |
% make |
% make |
515 |
\end{verbatim} |
\end{verbatim} |
525 |
% cd /scratch/exp2 |
% cd /scratch/exp2 |
526 |
% mkdir build |
% mkdir build |
527 |
% cd build |
% cd build |
528 |
% ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code |
% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ |
529 |
|
-mods=~/MITgcm/verification/exp2/code |
530 |
% make depend |
% make depend |
531 |
% make |
% make |
532 |
% cd ../ |
% cd ../ |
536 |
\end{verbatim} |
\end{verbatim} |
537 |
|
|
538 |
|
|
539 |
|
\subsection{Using \texttt{genmake2}} |
|
\subsection{\textit{genmake}} |
|
540 |
\label{sect:genmake} |
\label{sect:genmake} |
541 |
|
|
542 |
To compile the code, use the script \textit{genmake} located in the \textit{% |
To compile the code, first use the program \texttt{genmake2} (located |
543 |
tools} directory. \textit{genmake} is a script that generates the makefile. |
in the \texttt{tools} directory) to generate a Makefile. |
544 |
It has been written so that the code can be compiled on a wide diversity of |
\texttt{genmake2} is a shell script written to work with all |
545 |
machines and systems. However, if it doesn't work the first time on your |
``sh''--compatible shells including bash v1, bash v2, and Bourne. |
546 |
platform, you might need to edit certain lines of \textit{genmake} in the |
Internally, \texttt{genmake2} determines the locations of needed |
547 |
section containing the setups for the different machines. The file is |
files, the compiler, compiler options, libraries, and Unix tools. It |
548 |
structured like this: |
relies upon a number of ``optfiles'' located in the |
549 |
\begin{verbatim} |
\texttt{tools/build\_options} directory. |
550 |
. |
|
551 |
. |
The purpose of the optfiles is to provide all the compilation options |
552 |
. |
for particular ``platforms'' (where ``platform'' roughly means the |
553 |
general instructions (machine independent) |
combination of the hardware and the compiler) and code configurations. |
554 |
. |
Given the combinations of possible compilers and library dependencies |
555 |
. |
({\it eg.} MPI and NetCDF) there may be numerous optfiles available |
556 |
. |
for a single machine. The naming scheme for the majority of the |
557 |
- setup machine 1 |
optfiles shipped with the code is |
558 |
- setup machine 2 |
\begin{center} |
559 |
- setup machine 3 |
{\bf OS\_HARDWARE\_COMPILER } |
560 |
- setup machine 4 |
\end{center} |
561 |
etc |
where |
562 |
. |
\begin{description} |
563 |
. |
\item[OS] is the name of the operating system (generally the |
564 |
. |
lower-case output of the {\tt 'uname'} command) |
565 |
\end{verbatim} |
\item[HARDWARE] is a string that describes the CPU type and |
566 |
|
corresponds to output from the {\tt 'uname -m'} command: |
567 |
For example, the setup corresponding to a DEC alpha machine is reproduced |
\begin{description} |
568 |
here: |
\item[ia32] is for ``x86'' machines such as i386, i486, i586, i686, |
569 |
\begin{verbatim} |
and athlon |
570 |
case OSF1+mpi: |
\item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2) |
571 |
echo "Configuring for DEC Alpha" |
\item[amd64] is AMD x86\_64 systems |
572 |
set CPP = ( '/usr/bin/cpp -P' ) |
\item[ppc] is for Mac PowerPC systems |
573 |
set DEFINES = ( ${DEFINES} '-DTARGET_DEC -DWORDLENGTH=1' ) |
\end{description} |
574 |
set KPP = ( 'kapf' ) |
\item[COMPILER] is the compiler name (generally, the name of the |
575 |
set KPPFILES = ( 'main.F' ) |
FORTRAN executable) |
576 |
set KFLAGS1 = ( '-scan=132 -noconc -cmp=' ) |
\end{description} |
577 |
set FC = ( 'f77' ) |
|
578 |
set FFLAGS = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' ) |
In many cases, the default optfiles are sufficient and will result in |
579 |
set FOPTIM = ( '-O5 -fast -tune host -inline all' ) |
usable Makefiles. However, for some machines or code configurations, |
580 |
set NOOPTFLAGS = ( '-O0' ) |
new ``optfiles'' must be written. To create a new optfile, it is |
581 |
set LIBS = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' ) |
generally best to start with one of the defaults and modify it to suit |
582 |
set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F') |
your needs. Like \texttt{genmake2}, the optfiles are all written |
583 |
set RMFILES = ( '*.p.out' ) |
using a simple ``sh''--compatible syntax. While nearly all variables |
584 |
breaksw |
used within \texttt{genmake2} may be specified in the optfiles, the |
585 |
\end{verbatim} |
critical ones that should be defined are: |
586 |
|
|
587 |
Typically, these are the lines that you might need to edit to make \textit{% |
\begin{description} |
588 |
genmake} work on your platform if it doesn't work the first time. \textit{% |
\item[FC] the FORTRAN compiler (executable) to use |
589 |
genmake} understands several options that are described here: |
\item[DEFINES] the command-line DEFINE options passed to the compiler |
590 |
|
\item[CPP] the C pre-processor to use |
591 |
\begin{itemize} |
\item[NOOPTFLAGS] options flags for special files that should not be |
592 |
\item -rootdir=dir |
optimized |
593 |
|
\end{description} |
594 |
indicates where the model root directory is relative to the directory where |
|
595 |
you are compiling. This option is not needed if you compile in the \textit{% |
For example, the optfile for a typical Red Hat Linux machine (``ia32'' |
596 |
bin} directory (which is the default compilation directory) or within the |
architecture) using the GCC (g77) compiler is |
597 |
\textit{verification} tree. |
\begin{verbatim} |
598 |
|
FC=g77 |
599 |
\item -mods=dir1,dir2,... |
DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4' |
600 |
|
CPP='cpp -traditional -P' |
601 |
indicates the relative or absolute paths directories where the sources |
NOOPTFLAGS='-O0' |
602 |
should take precedence over the default versions (located in \textit{model}, |
# For IEEE, use the "-ffloat-store" option |
603 |
\textit{eesupp},...). Typically, this option is used when running the |
if test "x$IEEE" = x ; then |
604 |
examples, see below. |
FFLAGS='-Wimplicit -Wunused -Wuninitialized' |
605 |
|
FOPTIM='-O3 -malign-double -funroll-loops' |
606 |
\item -enable=pkg1,pkg2,... |
else |
607 |
|
FFLAGS='-Wimplicit -Wunused -ffloat-store' |
608 |
enables packages source code \textit{pkg1}, \textit{pkg2},... when creating |
FOPTIM='-O0 -malign-double' |
609 |
the makefile. |
fi |
610 |
|
\end{verbatim} |
611 |
\item -disable=pkg1,pkg2,... |
|
612 |
|
If you write an optfile for an unrepresented machine or compiler, you |
613 |
disables packages source code \textit{pkg1}, \textit{pkg2},... when creating |
are strongly encouraged to submit the optfile to the MITgcm project |
614 |
the makefile. |
for inclusion. Please send the file to the |
615 |
|
\begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml} |
616 |
\item -platform=machine |
\begin{center} |
617 |
|
MITgcm-support@mitgcm.org |
618 |
specifies the platform for which you want the makefile. In general, you |
\end{center} |
619 |
won't need this option. \textit{genmake} will select the right machine for |
\begin{rawhtml} </A> \end{rawhtml} |
620 |
you (the one you're working on!). However, this option is useful if you have |
mailing list. |
621 |
a choice of several compilers on one machine and you want to use the one |
|
622 |
that is not the default (ex: \texttt{pgf77} instead of \texttt{f77} under |
In addition to the optfiles, \texttt{genmake2} supports a number of |
623 |
Linux). |
helpful command-line options. A complete list of these options can be |
624 |
|
obtained from: |
625 |
\item -mpi |
\begin{verbatim} |
626 |
|
% genmake2 -h |
627 |
this is used when you want to run the model in parallel processing mode |
\end{verbatim} |
628 |
under mpi (see section on parallel computation for more details). |
|
629 |
|
The most important command-line options are: |
630 |
\item -jam |
\begin{description} |
631 |
|
|
632 |
this is used when you want to run the model in parallel processing mode |
\item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that |
633 |
under jam (see section on parallel computation for more details). |
should be used for a particular build. |
634 |
\end{itemize} |
|
635 |
|
If no "optfile" is specified (either through the command line or the |
636 |
For some of the examples, there is a file called \textit{.genmakerc} in the |
MITGCM\_OPTFILE environment variable), genmake2 will try to make a |
637 |
\textit{input} directory that has the relevant \textit{genmake} options for |
reasonable guess from the list provided in {\em |
638 |
that particular example. In this way you don't need to type the options when |
tools/build\_options}. The method used for making this guess is |
639 |
invoking \textit{genmake}. |
to first determine the combination of operating system and hardware |
640 |
|
(eg. "linux\_ia32") and then find a working FORTRAN compiler within |
641 |
|
the user's path. When these three items have been identified, |
642 |
|
genmake2 will try to find an optfile that has a matching name. |
643 |
|
|
644 |
|
\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default |
645 |
|
set of packages to be used. The normal order of precedence for |
646 |
|
packages is as follows: |
647 |
|
\begin{enumerate} |
648 |
|
\item If available, the command line (\texttt{--pdefault}) settings |
649 |
|
over-rule any others. |
650 |
|
|
651 |
|
\item Next, \texttt{genmake2} will look for a file named |
652 |
|
``\texttt{packages.conf}'' in the local directory or in any of the |
653 |
|
directories specified with the \texttt{--mods} option. |
654 |
|
|
655 |
|
\item Finally, if neither of the above are available, |
656 |
|
\texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file. |
657 |
|
\end{enumerate} |
658 |
|
|
659 |
|
\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file |
660 |
|
used for packages. |
661 |
|
|
662 |
|
If not specified, the default dependency file {\em pkg/pkg\_depend} |
663 |
|
is used. The syntax for this file is parsed on a line-by-line basis |
664 |
|
where each line containes either a comment ("\#") or a simple |
665 |
|
"PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol |
666 |
|
specifies a "must be used with" or a "must not be used with" |
667 |
|
relationship, respectively. If no rule is specified, then it is |
668 |
|
assumed that the two packages are compatible and will function |
669 |
|
either with or without each other. |
670 |
|
|
671 |
|
\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or |
672 |
|
automatic differentiation options file to be used. The file is |
673 |
|
analogous to the ``optfile'' defined above but it specifies |
674 |
|
information for the AD build process. |
675 |
|
|
676 |
|
The default file is located in {\em |
677 |
|
tools/adjoint\_options/adjoint\_default} and it defines the "TAF" |
678 |
|
and "TAMC" compilers. An alternate version is also available at |
679 |
|
{\em tools/adjoint\_options/adjoint\_staf} that selects the newer |
680 |
|
"STAF" compiler. As with any compilers, it is helpful to have their |
681 |
|
directories listed in your {\tt \$PATH} environment variable. |
682 |
|
|
683 |
|
\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of |
684 |
|
directories containing ``modifications''. These directories contain |
685 |
|
files with names that may (or may not) exist in the main MITgcm |
686 |
|
source tree but will be overridden by any identically-named sources |
687 |
|
within the ``MODS'' directories. |
688 |
|
|
689 |
|
The order of precedence for this "name-hiding" is as follows: |
690 |
|
\begin{itemize} |
691 |
|
\item ``MODS'' directories (in the order given) |
692 |
|
\item Packages either explicitly specified or provided by default |
693 |
|
(in the order given) |
694 |
|
\item Packages included due to package dependencies (in the order |
695 |
|
that that package dependencies are parsed) |
696 |
|
\item The "standard dirs" (which may have been specified by the |
697 |
|
``-standarddirs'' option) |
698 |
|
\end{itemize} |
699 |
|
|
700 |
|
\item[\texttt{--mpi}] This option enables certain MPI features (using |
701 |
|
CPP \texttt{\#define}s) within the code and is necessary for MPI |
702 |
|
builds (see Section \ref{sect:mpi-build}). |
703 |
|
|
704 |
|
\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of |
705 |
|
soft-links and other bugs common with the \texttt{make} versions |
706 |
|
provided by commercial Unix vendors, GNU \texttt{make} (sometimes |
707 |
|
called \texttt{gmake}) should be preferred. This option provides a |
708 |
|
means for specifying the make executable to be used. |
709 |
|
|
710 |
|
\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX) |
711 |
|
machines, the ``bash'' shell is unavailable. To run on these |
712 |
|
systems, \texttt{genmake2} can be invoked using an ``sh'' (that is, |
713 |
|
a Bourne, POSIX, or compatible) shell. The syntax in these |
714 |
|
circumstances is: |
715 |
|
\begin{center} |
716 |
|
\texttt{\% /bin/sh genmake2 -bash=/bin/sh [...options...]} |
717 |
|
\end{center} |
718 |
|
where \texttt{/bin/sh} can be replaced with the full path and name |
719 |
|
of the desired shell. |
720 |
|
|
721 |
|
\end{description} |
722 |
|
|
723 |
|
|
724 |
|
\subsection{Building with MPI} |
725 |
|
\label{sect:mpi-build} |
726 |
|
|
727 |
|
Building MITgcm to use MPI libraries can be complicated due to the |
728 |
|
variety of different MPI implementations available, their dependencies |
729 |
|
or interactions with different compilers, and their often ad-hoc |
730 |
|
locations within file systems. For these reasons, its generally a |
731 |
|
good idea to start by finding and reading the documentation for your |
732 |
|
machine(s) and, if necessary, seeking help from your local systems |
733 |
|
administrator. |
734 |
|
|
735 |
|
The steps for building MITgcm with MPI support are: |
736 |
|
\begin{enumerate} |
737 |
|
|
738 |
|
\item Determine the locations of your MPI-enabled compiler and/or MPI |
739 |
|
libraries and put them into an options file as described in Section |
740 |
|
\ref{sect:genmake}. One can start with one of the examples in: |
741 |
|
\begin{rawhtml} <A |
742 |
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/"> |
743 |
|
\end{rawhtml} |
744 |
|
\begin{center} |
745 |
|
\texttt{MITgcm/tools/build\_options/} |
746 |
|
\end{center} |
747 |
|
\begin{rawhtml} </A> \end{rawhtml} |
748 |
|
such as \texttt{linux\_ia32\_g77+mpi\_cg01} or |
749 |
|
\texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at |
750 |
|
hand. You may need help from your user guide or local systems |
751 |
|
administrator to determine the exact location of the MPI libraries. |
752 |
|
If libraries are not installed, MPI implementations and related |
753 |
|
tools are available including: |
754 |
|
\begin{itemize} |
755 |
|
\item \begin{rawhtml} <A |
756 |
|
href="http://www-unix.mcs.anl.gov/mpi/mpich/"> |
757 |
|
\end{rawhtml} |
758 |
|
MPICH |
759 |
|
\begin{rawhtml} </A> \end{rawhtml} |
760 |
|
|
761 |
|
\item \begin{rawhtml} <A |
762 |
|
href="http://www.lam-mpi.org/"> |
763 |
|
\end{rawhtml} |
764 |
|
LAM/MPI |
765 |
|
\begin{rawhtml} </A> \end{rawhtml} |
766 |
|
|
767 |
|
\item \begin{rawhtml} <A |
768 |
|
href="http://www.osc.edu/~pw/mpiexec/"> |
769 |
|
\end{rawhtml} |
770 |
|
MPIexec |
771 |
|
\begin{rawhtml} </A> \end{rawhtml} |
772 |
|
\end{itemize} |
773 |
|
|
774 |
|
\item Build the code with the \texttt{genmake2} \texttt{-mpi} option |
775 |
|
(see Section \ref{sect:genmake}) using commands such as: |
776 |
|
{\footnotesize \begin{verbatim} |
777 |
|
% ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE |
778 |
|
% make depend |
779 |
|
% make |
780 |
|
\end{verbatim} } |
781 |
|
|
782 |
|
\item Run the code with the appropriate MPI ``run'' or ``exec'' |
783 |
|
program provided with your particular implementation of MPI. |
784 |
|
Typical MPI packages such as MPICH will use something like: |
785 |
|
\begin{verbatim} |
786 |
|
% mpirun -np 4 -machinefile mf ./mitgcmuv |
787 |
|
\end{verbatim} |
788 |
|
Sightly more complicated scripts may be needed for many machines |
789 |
|
since execution of the code may be controlled by both the MPI |
790 |
|
library and a job scheduling and queueing system such as PBS, |
791 |
|
LoadLeveller, Condor, or any of a number of similar tools. A few |
792 |
|
example scripts (those used for our \begin{rawhtml} <A |
793 |
|
href="http://mitgcm.org/testing.html"> \end{rawhtml}regular |
794 |
|
verification runs\begin{rawhtml} </A> \end{rawhtml}) are available |
795 |
|
at: |
796 |
|
\begin{rawhtml} <A |
797 |
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/"> |
798 |
|
\end{rawhtml} |
799 |
|
{\footnotesize \tt |
800 |
|
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ } |
801 |
|
\begin{rawhtml} </A> \end{rawhtml} |
802 |
|
|
803 |
|
\end{enumerate} |
804 |
|
|
805 |
|
An example of the above process on the MITgcm cluster (``cg01'') using |
806 |
|
the GNU g77 compiler and the mpich MPI library is: |
807 |
|
|
808 |
|
{\footnotesize \begin{verbatim} |
809 |
|
% cd MITgcm/verification/exp5 |
810 |
|
% mkdir build |
811 |
|
% cd build |
812 |
|
% ../../../tools/genmake2 -mpi -mods=../code \ |
813 |
|
-of=../../../tools/build_options/linux_ia32_g77+mpi_cg01 |
814 |
|
% make depend |
815 |
|
% make |
816 |
|
% cd ../input |
817 |
|
% /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \ |
818 |
|
-machinefile mf --gm-kill 5 -v -np 2 ../build/mitgcmuv |
819 |
|
\end{verbatim} } |
820 |
|
|
821 |
\section{Running the model} |
\section[Running MITgcm]{Running the model in prognostic mode} |
822 |
\label{sect:runModel} |
\label{sect:runModel} |
823 |
|
\begin{rawhtml} |
824 |
|
<!-- CMIREDIR:runModel: --> |
825 |
|
\end{rawhtml} |
826 |
|
|
827 |
|
If compilation finished succesfully (section \ref{sect:buildingCode}) |
828 |
|
then an executable called \texttt{mitgcmuv} will now exist in the |
829 |
|
local directory. |
830 |
|
|
831 |
If compilation finished succesfuully (section \ref{sect:buildModel}) |
To run the model as a single process (\textit{ie.} not in parallel) |
832 |
then an executable called {\em mitgcmuv} will now exist in the local |
simply type: |
|
directory. |
|
|
|
|
|
To run the model as a single process (ie. not in parallel) simply |
|
|
type: |
|
833 |
\begin{verbatim} |
\begin{verbatim} |
834 |
% ./mitgcmuv |
% ./mitgcmuv |
835 |
\end{verbatim} |
\end{verbatim} |
839 |
your screen. This output contains details such as parameter values as |
your screen. This output contains details such as parameter values as |
840 |
well as diagnostics such as mean Kinetic energy, largest CFL number, |
well as diagnostics such as mean Kinetic energy, largest CFL number, |
841 |
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 |
842 |
normally re-direct the {\em stdout} stream as follows: |
normally re-direct the \texttt{stdout} stream as follows: |
843 |
\begin{verbatim} |
\begin{verbatim} |
844 |
% ./mitgcmuv > output.txt |
% ./mitgcmuv > output.txt |
845 |
\end{verbatim} |
\end{verbatim} |
846 |
|
In the event that the model encounters an error and stops, it is very |
847 |
For the example experiments in {\em vericication}, an example of the |
helpful to include the last few line of this \texttt{output.txt} file |
848 |
output is kept in {\em results/output.txt} for comparison. You can compare |
along with the (\texttt{stderr}) error message within any bug reports. |
849 |
your {\em output.txt} with this one to check that the set-up works. |
|
850 |
|
For the example experiments in \texttt{verification}, an example of the |
851 |
|
output is kept in \texttt{results/output.txt} for comparison. You can |
852 |
|
compare your \texttt{output.txt} with the corresponding one for that |
853 |
|
experiment to check that the set-up works. |
854 |
|
|
855 |
|
|
856 |
|
|
857 |
\subsection{Output files} |
\subsection{Output files} |
858 |
|
|
859 |
The model produces various output files. At a minimum, the instantaneous |
The model produces various output files and, when using \texttt{mnc}, |
860 |
``state'' of the model is written out, which is made of the following files: |
sometimes even directories. Depending upon the I/O package(s) |
861 |
|
selected at compile time (either \texttt{mdsio} or \texttt{mnc} or |
862 |
|
both as determined by \texttt{code/packages.conf}) and the run-time |
863 |
|
flags set (in \texttt{input/data.pkg}), the following output may |
864 |
|
appear. |
865 |
|
|
866 |
|
|
867 |
|
\subsubsection{MDSIO output files} |
868 |
|
|
869 |
|
The ``traditional'' output files are generated by the \texttt{mdsio} |
870 |
|
package. At a minimum, the instantaneous ``state'' of the model is |
871 |
|
written out, which is made of the following files: |
872 |
|
|
873 |
\begin{itemize} |
\begin{itemize} |
874 |
\item \textit{U.00000nIter} - zonal component of velocity field (m/s and $> |
\item \texttt{U.00000nIter} - zonal component of velocity field (m/s |
875 |
0 $ eastward). |
and positive eastward). |
876 |
|
|
877 |
\item \textit{V.00000nIter} - meridional component of velocity field (m/s |
\item \texttt{V.00000nIter} - meridional component of velocity field |
878 |
and $> 0$ northward). |
(m/s and positive northward). |
879 |
|
|
880 |
\item \textit{W.00000nIter} - vertical component of velocity field (ocean: |
\item \texttt{W.00000nIter} - vertical component of velocity field |
881 |
m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure |
(ocean: m/s and positive upward, atmosphere: Pa/s and positive |
882 |
i.e. downward). |
towards increasing pressure i.e. downward). |
883 |
|
|
884 |
\item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C, |
\item \texttt{T.00000nIter} - potential temperature (ocean: |
885 |
atmosphere: $^{0}$K). |
$^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$). |
886 |
|
|
887 |
\item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor |
\item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water |
888 |
(g/kg). |
vapor (g/kg). |
889 |
|
|
890 |
\item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere: |
\item \texttt{Eta.00000nIter} - ocean: surface elevation (m), |
891 |
surface pressure anomaly (Pa). |
atmosphere: surface pressure anomaly (Pa). |
892 |
\end{itemize} |
\end{itemize} |
893 |
|
|
894 |
The chain \textit{00000nIter} consists of ten figures that specify the |
The chain \texttt{00000nIter} consists of ten figures that specify the |
895 |
iteration number at which the output is written out. For example, \textit{% |
iteration number at which the output is written out. For example, |
896 |
U.0000000300} is the zonal velocity at iteration 300. |
\texttt{U.0000000300} is the zonal velocity at iteration 300. |
897 |
|
|
898 |
In addition, a ``pickup'' or ``checkpoint'' file called: |
In addition, a ``pickup'' or ``checkpoint'' file called: |
899 |
|
|
900 |
\begin{itemize} |
\begin{itemize} |
901 |
\item \textit{pickup.00000nIter} |
\item \texttt{pickup.00000nIter} |
902 |
\end{itemize} |
\end{itemize} |
903 |
|
|
904 |
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 |
906 |
there is an additional ``pickup'' file: |
there is an additional ``pickup'' file: |
907 |
|
|
908 |
\begin{itemize} |
\begin{itemize} |
909 |
\item \textit{pickup\_cd.00000nIter} |
\item \texttt{pickup\_cd.00000nIter} |
910 |
\end{itemize} |
\end{itemize} |
911 |
|
|
912 |
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 |
913 |
in order to restart the integration. Rolling checkpoint files are the same |
in order to restart the integration. Rolling checkpoint files are the same |
914 |
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 |
915 |
\textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be |
\texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be |
916 |
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 |
917 |
output to save disk space during long integrations. |
output to save disk space during long integrations. |
918 |
|
|
919 |
|
|
920 |
|
|
921 |
|
\subsubsection{MNC output files} |
922 |
|
|
923 |
|
Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output |
924 |
|
is usually (though not necessarily) placed within a subdirectory with |
925 |
|
a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}. The files |
926 |
|
within this subdirectory are all in the ``self-describing'' netCDF |
927 |
|
format and can thus be browsed and/or plotted using tools such as: |
928 |
|
\begin{itemize} |
929 |
|
\item \texttt{ncdump} is a utility which is typically included |
930 |
|
with every netCDF install: |
931 |
|
\begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml} |
932 |
|
\begin{verbatim} |
933 |
|
http://www.unidata.ucar.edu/packages/netcdf/ |
934 |
|
\end{verbatim} |
935 |
|
\begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF |
936 |
|
binaries into formatted ASCII text files. |
937 |
|
|
938 |
|
\item \texttt{ncview} utility is a very convenient and quick way |
939 |
|
to plot netCDF data and it runs on most OSes: |
940 |
|
\begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml} |
941 |
|
\begin{verbatim} |
942 |
|
http://meteora.ucsd.edu/~pierce/ncview_home_page.html |
943 |
|
\end{verbatim} |
944 |
|
\begin{rawhtml} </A> \end{rawhtml} |
945 |
|
|
946 |
|
\item MatLAB(c) and other common post-processing environments provide |
947 |
|
various netCDF interfaces including: |
948 |
|
\begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml} |
949 |
|
\begin{verbatim} |
950 |
|
http://mexcdf.sourceforge.net/ |
951 |
|
\end{verbatim} |
952 |
|
\begin{rawhtml} </A> \end{rawhtml} |
953 |
|
\begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml} |
954 |
|
\begin{verbatim} |
955 |
|
http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html |
956 |
|
\end{verbatim} |
957 |
|
\begin{rawhtml} </A> \end{rawhtml} |
958 |
|
\end{itemize} |
959 |
|
|
960 |
|
|
961 |
\subsection{Looking at the output} |
\subsection{Looking at the output} |
962 |
|
|
963 |
All the model data are written according to a ``meta/data'' file format. |
The ``traditional'' or mdsio model data are written according to a |
964 |
Each variable is associated with two files with suffix names \textit{.data} |
``meta/data'' file format. Each variable is associated with two files |
965 |
and \textit{.meta}. The \textit{.data} file contains the data written in |
with suffix names \texttt{.data} and \texttt{.meta}. The |
966 |
binary form (big\_endian by default). The \textit{.meta} file is a |
\texttt{.data} file contains the data written in binary form |
967 |
``header'' file that contains information about the size and the structure |
(big\_endian by default). The \texttt{.meta} file is a ``header'' file |
968 |
of the \textit{.data} file. This way of organizing the output is |
that contains information about the size and the structure of the |
969 |
particularly useful when running multi-processors calculations. The base |
\texttt{.data} file. This way of organizing the output is particularly |
970 |
version of the model includes a few matlab utilities to read output files |
useful when running multi-processors calculations. The base version of |
971 |
written in this format. The matlab scripts are located in the directory |
the model includes a few matlab utilities to read output files written |
972 |
\textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads |
in this format. The matlab scripts are located in the directory |
973 |
the data. Look at the comments inside the script to see how to use it. |
\texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m} |
974 |
|
reads the data. Look at the comments inside the script to see how to |
975 |
|
use it. |
976 |
|
|
977 |
Some examples of reading and visualizing some output in {\em Matlab}: |
Some examples of reading and visualizing some output in {\em Matlab}: |
978 |
\begin{verbatim} |
\begin{verbatim} |
989 |
>> 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 |
990 |
\end{verbatim} |
\end{verbatim} |
991 |
|
|
992 |
\section{Doing it yourself: customizing the code} |
Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and |
993 |
|
they are described in Section \ref{sec:pkg:mnc}. |
|
When you are ready to run the model in the configuration you want, the |
|
|
easiest thing is to use and adapt the setup of the case studies experiment |
|
|
(described previously) that is the closest to your configuration. Then, the |
|
|
amount of setup will be minimized. In this section, we focus on the setup |
|
|
relative to the ''numerical model'' part of the code (the setup relative to |
|
|
the ''execution environment'' part is covered in the parallel implementation |
|
|
section) and on the variables and parameters that you are likely to change. |
|
|
|
|
|
\subsection{Configuration and setup} |
|
|
|
|
|
The CPP keys relative to the ''numerical model'' part of the code are all |
|
|
defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{% |
|
|
model/inc }or in one of the \textit{code }directories of the case study |
|
|
experiments under \textit{verification.} The model parameters are defined |
|
|
and declared in the file \textit{model/inc/PARAMS.h }and their default |
|
|
values are set in the routine \textit{model/src/set\_defaults.F. }The |
|
|
default values can be modified in the namelist file \textit{data }which |
|
|
needs to be located in the directory where you will run the model. The |
|
|
parameters are initialized in the routine \textit{model/src/ini\_parms.F}. |
|
|
Look at this routine to see in what part of the namelist the parameters are |
|
|
located. |
|
|
|
|
|
In what follows the parameters are grouped into categories related to the |
|
|
computational domain, the equations solved in the model, and the simulation |
|
|
controls. |
|
|
|
|
|
\subsection{Computational domain, geometry and time-discretization} |
|
|
|
|
|
\begin{itemize} |
|
|
\item dimensions |
|
|
\end{itemize} |
|
|
|
|
|
The number of points in the x, y,\textit{\ }and r\textit{\ }directions are |
|
|
represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }% |
|
|
and \textbf{Nr}\textit{\ }respectively which are declared and set in the |
|
|
file \textit{model/inc/SIZE.h. }(Again, this assumes a mono-processor |
|
|
calculation. For multiprocessor calculations see section on parallel |
|
|
implementation.) |
|
|
|
|
|
\begin{itemize} |
|
|
\item grid |
|
|
\end{itemize} |
|
|
|
|
|
Three different grids are available: cartesian, spherical polar, and |
|
|
curvilinear (including the cubed sphere). The grid is set through the |
|
|
logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{% |
|
|
usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{% |
|
|
usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear |
|
|
grids, the southern boundary is defined through the variable \textbf{phiMin}% |
|
|
\textit{\ }which corresponds to the latitude of the southern most cell face |
|
|
(in degrees). The resolution along the x and y directions is controlled by |
|
|
the 1D arrays \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters |
|
|
in the case of a cartesian grid, in degrees otherwise). The vertical grid |
|
|
spacing is set through the 1D array \textbf{delz }for the ocean (in meters) |
|
|
or \textbf{delp}\textit{\ }for the atmosphere (in Pa). The variable \textbf{% |
|
|
Ro\_SeaLevel} represents the standard position of Sea-Level in ''R'' |
|
|
coordinate. This is typically set to 0m for the ocean (default value) and 10$% |
|
|
^{5}$Pa for the atmosphere. For the atmosphere, also set the logical |
|
|
variable \textbf{groundAtK1} to '.\texttt{TRUE}.'. which put the first level |
|
|
(k=1) at the lower boundary (ground). |
|
|
|
|
|
For the cartesian grid case, the Coriolis parameter $f$ is set through the |
|
|
variables \textbf{f0}\textit{\ }and \textbf{beta}\textit{\ }which correspond |
|
|
to the reference Coriolis parameter (in s$^{-1}$) and $\frac{\partial f}{% |
|
|
\partial y}$(in m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ }% |
|
|
is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the |
|
|
southern edge of the domain. |
|
|
|
|
|
\begin{itemize} |
|
|
\item topography - full and partial cells |
|
|
\end{itemize} |
|
|
|
|
|
The domain bathymetry is read from a file that contains a 2D (x,y) map of |
|
|
depths (in m) for the ocean or pressures (in Pa) for the atmosphere. The |
|
|
file name is represented by the variable \textbf{bathyFile}\textit{. }The |
|
|
file is assumed to contain binary numbers giving the depth (pressure) of the |
|
|
model at each grid cell, ordered with the x coordinate varying fastest. The |
|
|
points are ordered from low coordinate to high coordinate for both axes. The |
|
|
model code applies without modification to enclosed, periodic, and double |
|
|
periodic domains. Periodicity is assumed by default and is suppressed by |
|
|
setting the depths to 0m for the cells at the limits of the computational |
|
|
domain (note: not sure this is the case for the atmosphere). The precision |
|
|
with which to read the binary data is controlled by the integer variable |
|
|
\textbf{readBinaryPrec }which can take the value \texttt{32} (single |
|
|
precision) or \texttt{64} (double precision). See the matlab program \textit{% |
|
|
gendata.m }in the \textit{input }directories under \textit{verification }to |
|
|
see how the bathymetry files are generated for the case study experiments. |
|
|
|
|
|
To use the partial cell capability, the variable \textbf{hFacMin}\textit{\ }% |
|
|
needs to be set to a value between 0 and 1 (it is set to 1 by default) |
|
|
corresponding to the minimum fractional size of the cell. For example if the |
|
|
bottom cell is 500m thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the |
|
|
actual thickness of the cell (i.e. used in the code) can cover a range of |
|
|
discrete values 50m apart from 50m to 500m depending on the value of the |
|
|
bottom depth (in \textbf{bathyFile}) at this point. |
|
|
|
|
|
Note that the bottom depths (or pressures) need not coincide with the models |
|
|
levels as deduced from \textbf{delz}\textit{\ }or\textit{\ }\textbf{delp}% |
|
|
\textit{. }The model will interpolate the numbers in \textbf{bathyFile}% |
|
|
\textit{\ }so that they match the levels obtained from \textbf{delz}\textit{% |
|
|
\ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. } |
|
|
|
|
|
(Note: the atmospheric case is a bit more complicated than what is written |
|
|
here I think. To come soon...) |
|
|
|
|
|
\begin{itemize} |
|
|
\item time-discretization |
|
|
\end{itemize} |
|
|
|
|
|
The time steps are set through the real variables \textbf{deltaTMom }and |
|
|
\textbf{deltaTtracer }(in s) which represent the time step for the momentum |
|
|
and tracer equations, respectively. For synchronous integrations, simply set |
|
|
the two variables to the same value (or you can prescribe one time step only |
|
|
through the variable \textbf{deltaT}). The Adams-Bashforth stabilizing |
|
|
parameter is set through the variable \textbf{abEps }(dimensionless). The |
|
|
stagger baroclinic time stepping can be activated by setting the logical |
|
|
variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'. |
|
|
|
|
|
\subsection{Equation of state} |
|
|
|
|
|
First, because the model equations are written in terms of perturbations, a |
|
|
reference thermodynamic state needs to be specified. This is done through |
|
|
the 1D arrays \textbf{tRef}\textit{\ }and \textbf{sRef}. \textbf{tRef }% |
|
|
specifies the reference potential temperature profile (in $^{o}$C for |
|
|
the ocean and $^{o}$K for the atmosphere) starting from the level |
|
|
k=1. Similarly, \textbf{sRef}\textit{\ }specifies the reference salinity |
|
|
profile (in ppt) for the ocean or the reference specific humidity profile |
|
|
(in g/kg) for the atmosphere. |
|
|
|
|
|
The form of the equation of state is controlled by the character variables |
|
|
\textbf{buoyancyRelation}\textit{\ }and \textbf{eosType}\textit{. }\textbf{% |
|
|
buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and |
|
|
needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In |
|
|
this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'. |
|
|
For the ocean, two forms of the equation of state are available: linear (set |
|
|
\textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial |
|
|
approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\ |
|
|
}to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the |
|
|
thermal and haline expansion coefficients represented by the variables |
|
|
\textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(in ppt$% |
|
|
^{-1}$). For the nonlinear case, you need to generate a file of polynomial |
|
|
coefficients called \textit{POLY3.COEFFS. }To do this, use the program |
|
|
\textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is |
|
|
available in the same directory and you will need to edit the number and the |
|
|
values of the vertical levels in \textit{knudsen2.f }so that they match |
|
|
those of your configuration). \textit{\ } |
|
|
|
|
|
\subsection{Momentum equations} |
|
|
|
|
|
In this section, we only focus for now on the parameters that you are likely |
|
|
to change, i.e. the ones relative to forcing and dissipation for example. |
|
|
The details relevant to the vector-invariant form of the equations and the |
|
|
various advection schemes are not covered for the moment. We assume that you |
|
|
use the standard form of the momentum equations (i.e. the flux-form) with |
|
|
the default advection scheme. Also, there are a few logical variables that |
|
|
allow you to turn on/off various terms in the momentum equation. These |
|
|
variables are called \textbf{momViscosity, momAdvection, momForcing, |
|
|
useCoriolis, momPressureForcing, momStepping}\textit{, }and \textit{\ }% |
|
|
\textbf{metricTerms }and are assumed to be set to '.\texttt{TRUE}.' here. |
|
|
Look at the file \textit{model/inc/PARAMS.h }for a precise definition of |
|
|
these variables. |
|
|
|
|
|
\begin{itemize} |
|
|
\item initialization |
|
|
\end{itemize} |
|
|
|
|
|
The velocity components are initialized to 0 unless the simulation is |
|
|
starting from a pickup file (see section on simulation control parameters). |
|
|
|
|
|
\begin{itemize} |
|
|
\item forcing |
|
|
\end{itemize} |
|
|
|
|
|
This section only applies to the ocean. You need to generate wind-stress |
|
|
data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{% |
|
|
meridWindFile }corresponding to the zonal and meridional components of the |
|
|
wind stress, respectively (if you want the stress to be along the direction |
|
|
of only one of the model horizontal axes, you only need to generate one |
|
|
file). The format of the files is similar to the bathymetry file. The zonal |
|
|
(meridional) stress data are assumed to be in Pa and located at U-points |
|
|
(V-points). As for the bathymetry, the precision with which to read the |
|
|
binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } |
|
|
See the matlab program \textit{gendata.m }in the \textit{input }directories |
|
|
under \textit{verification }to see how simple analytical wind forcing data |
|
|
are generated for the case study experiments. |
|
|
|
|
|
There is also the possibility of prescribing time-dependent periodic |
|
|
forcing. To do this, concatenate the successive time records into a single |
|
|
file (for each stress component) ordered in a (x, y, t) fashion and set the |
|
|
following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.', |
|
|
\textbf{externForcingPeriod }to the period (in s) of which the forcing |
|
|
varies (typically 1 month), and \textbf{externForcingCycle }to the repeat |
|
|
time (in s) of the forcing (typically 1 year -- note: \textbf{% |
|
|
externForcingCycle }must be a multiple of \textbf{externForcingPeriod}). |
|
|
With these variables set up, the model will interpolate the forcing linearly |
|
|
at each iteration. |
|
|
|
|
|
\begin{itemize} |
|
|
\item dissipation |
|
|
\end{itemize} |
|
|
|
|
|
The lateral eddy viscosity coefficient is specified through the variable |
|
|
\textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity |
|
|
coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$% |
|
|
^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) |
|
|
for the atmosphere. The vertical diffusive fluxes can be computed implicitly |
|
|
by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}% |
|
|
.'. In addition, biharmonic mixing can be added as well through the variable |
|
|
\textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid, |
|
|
you might also need to set the variable \textbf{cosPower} which is set to 0 |
|
|
by default and which represents the power of cosine of latitude to multiply |
|
|
viscosity. Slip or no-slip conditions at lateral and bottom boundaries are |
|
|
specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }% |
|
|
and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip |
|
|
boundary conditions are applied. If no-slip boundary conditions are applied |
|
|
at the bottom, a bottom drag can be applied as well. Two forms are |
|
|
available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$% |
|
|
^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{% |
|
|
\ }in m$^{-1}$). |
|
|
|
|
|
The Fourier and Shapiro filters are described elsewhere. |
|
|
|
|
|
\begin{itemize} |
|
|
\item C-D scheme |
|
|
\end{itemize} |
|
|
|
|
|
If you run at a sufficiently coarse resolution, you will need the C-D scheme |
|
|
for the computation of the Coriolis terms. The variable\textbf{\ tauCD}, |
|
|
which represents the C-D scheme coupling timescale (in s) needs to be set. |
|
|
|
|
|
\begin{itemize} |
|
|
\item calculation of pressure/geopotential |
|
|
\end{itemize} |
|
|
|
|
|
First, to run a non-hydrostatic ocean simulation, set the logical variable |
|
|
\textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure field is then |
|
|
inverted through a 3D elliptic equation. (Note: this capability is not |
|
|
available for the atmosphere yet.) By default, a hydrostatic simulation is |
|
|
assumed and a 2D elliptic equation is used to invert the pressure field. The |
|
|
parameters controlling the behaviour of the elliptic solvers are the |
|
|
variables \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual }% |
|
|
for the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{% |
|
|
cg3dTargetResidual }for the 3D case. You probably won't need to alter the |
|
|
default values (are we sure of this?). |
|
|
|
|
|
For the calculation of the surface pressure (for the ocean) or surface |
|
|
geopotential (for the atmosphere) you need to set the logical variables |
|
|
\textbf{rigidLid} and \textbf{implicitFreeSurface}\textit{\ }(set one to '.% |
|
|
\texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you |
|
|
want to deal with the ocean upper or atmosphere lower boundary). |
|
|
|
|
|
\subsection{Tracer equations} |
|
|
|
|
|
This section covers the tracer equations i.e. the potential temperature |
|
|
equation and the salinity (for the ocean) or specific humidity (for the |
|
|
atmosphere) equation. As for the momentum equations, we only describe for |
|
|
now the parameters that you are likely to change. The logical variables |
|
|
\textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{% |
|
|
tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off |
|
|
terms in the temperature equation (same thing for salinity or specific |
|
|
humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{% |
|
|
saltAdvection}\textit{\ }etc). These variables are all assumed here to be |
|
|
set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a |
|
|
precise definition. |
|
|
|
|
|
\begin{itemize} |
|
|
\item initialization |
|
|
\end{itemize} |
|
|
|
|
|
The initial tracer data can be contained in the binary files \textbf{% |
|
|
hydrogThetaFile }and \textbf{hydrogSaltFile}. These files should contain 3D |
|
|
data ordered in an (x, y, r) fashion with k=1 as the first vertical level. |
|
|
If no file names are provided, the tracers are then initialized with the |
|
|
values of \textbf{tRef }and \textbf{sRef }mentioned above (in the equation |
|
|
of state section). In this case, the initial tracer data are uniform in x |
|
|
and y for each depth level. |
|
|
|
|
|
\begin{itemize} |
|
|
\item forcing |
|
|
\end{itemize} |
|
|
|
|
|
This part is more relevant for the ocean, the procedure for the atmosphere |
|
|
not being completely stabilized at the moment. |
|
|
|
|
|
A combination of fluxes data and relaxation terms can be used for driving |
|
|
the tracer equations. \ For potential temperature, heat flux data (in W/m$% |
|
|
^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }% |
|
|
Alternatively or in addition, the forcing can be specified through a |
|
|
relaxation term. The SST data to which the model surface temperatures are |
|
|
restored to are supposed to be stored in the 2D binary file \textbf{% |
|
|
thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient |
|
|
is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The |
|
|
same procedure applies for salinity with the variable names \textbf{EmPmRfile% |
|
|
}\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}% |
|
|
\textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data |
|
|
files and relaxation time scale coefficient (in s), respectively. Also for |
|
|
salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural |
|
|
boundary conditions are applied i.e. when computing the surface salinity |
|
|
tendency, the freshwater flux is multiplied by the model surface salinity |
|
|
instead of a constant salinity value. |
|
|
|
|
|
As for the other input files, the precision with which to read the data is |
|
|
controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic |
|
|
forcing can be applied as well following the same procedure used for the |
|
|
wind forcing data (see above). |
|
|
|
|
|
\begin{itemize} |
|
|
\item dissipation |
|
|
\end{itemize} |
|
|
|
|
|
Lateral eddy diffusivities for temperature and salinity/specific humidity |
|
|
are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }% |
|
|
(in m$^{2}$/s). Vertical eddy diffusivities are specified through the |
|
|
variables \textbf{diffKzT }and \textbf{diffKzS }(in m$^{2}$/s) for the ocean |
|
|
and \textbf{diffKpT }and \textbf{diffKpS }(in Pa$^{2}$/s) for the |
|
|
atmosphere. The vertical diffusive fluxes can be computed implicitly by |
|
|
setting the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}% |
|
|
.'. In addition, biharmonic diffusivities can be specified as well through |
|
|
the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in m$^{4}$/s). Note |
|
|
that the cosine power scaling (specified through \textbf{cosPower }- see the |
|
|
momentum equations section) is applied to the tracer diffusivities |
|
|
(Laplacian and biharmonic) as well. The Gent and McWilliams parameterization |
|
|
for oceanic tracers is described in the package section. Finally, note that |
|
|
tracers can be also subject to Fourier and Shapiro filtering (see the |
|
|
corresponding section on these filters). |
|
|
|
|
|
\begin{itemize} |
|
|
\item ocean convection |
|
|
\end{itemize} |
|
|
|
|
|
Two options are available to parameterize ocean convection: one is to use |
|
|
the convective adjustment scheme. In this case, you need to set the variable |
|
|
\textbf{cadjFreq}, which represents the frequency (in s) with which the |
|
|
adjustment algorithm is called, to a non-zero value (if set to a negative |
|
|
value by the user, the model will set it to the tracer time step). The other |
|
|
option is to parameterize convection with implicit vertical diffusion. To do |
|
|
this, set the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}% |
|
|
.' and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s) you |
|
|
wish the tracer vertical diffusivities to have when mixing tracers |
|
|
vertically due to static instabilities. Note that \textbf{cadjFreq }and |
|
|
\textbf{ivdc\_kappa }can not both have non-zero value. |
|
|
|
|
|
\subsection{Simulation controls} |
|
|
|
|
|
The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s) |
|
|
which determines the IO frequencies and is used in tagging output. |
|
|
Typically, you will set it to the tracer time step for accelerated runs |
|
|
(otherwise it is simply set to the default time step \textbf{deltaT}). |
|
|
Frequency of checkpointing and dumping of the model state are referenced to |
|
|
this clock (see below). |
|
|
|
|
|
\begin{itemize} |
|
|
\item run duration |
|
|
\end{itemize} |
|
|
|
|
|
The beginning of a simulation is set by specifying a start time (in s) |
|
|
through the real variable \textbf{startTime }or by specifying an initial |
|
|
iteration number through the integer variable \textbf{nIter0}. If these |
|
|
variables are set to nonzero values, the model will look for a ''pickup'' |
|
|
file \textit{pickup.0000nIter0 }to restart the integration\textit{. }The end |
|
|
of a simulation is set through the real variable \textbf{endTime }(in s). |
|
|
Alternatively, you can specify instead the number of time steps to execute |
|
|
through the integer variable \textbf{nTimeSteps}. |
|
|
|
|
|
\begin{itemize} |
|
|
\item frequency of output |
|
|
\end{itemize} |
|
994 |
|
|
|
Real variables defining frequencies (in s) with which output files are |
|
|
written on disk need to be set up. \textbf{dumpFreq }controls the frequency |
|
|
with which the instantaneous state of the model is saved. \textbf{chkPtFreq }% |
|
|
and \textbf{pchkPtFreq }control the output frequency of rolling and |
|
|
permanent checkpoint files, respectively. See section 1.5.1 Output files for the |
|
|
definition of model state and checkpoint files. In addition, time-averaged |
|
|
fields can be written out by setting the variable \textbf{taveFreq} (in s). |
|
|
The precision with which to write the binary data is controlled by the |
|
|
integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{% |
|
|
64}). |
|