| 17 |
|
|
| 18 |
\section{Where to find information} |
\section{Where to find information} |
| 19 |
\label{sect:whereToFindInfo} |
\label{sect:whereToFindInfo} |
| 20 |
|
\begin{rawhtml} |
| 21 |
A web site is maintained for release 1 (Sealion) of MITgcm: |
<!-- CMIREDIR:whereToFindInfo: --> |
| 22 |
\begin{verbatim} |
\end{rawhtml} |
| 23 |
http://mitgcm.org/sealion |
|
| 24 |
\end{verbatim} |
There is a web-archived support mailing list for the model that |
| 25 |
Here you will find an on-line version of this document, a |
you can email at \texttt{MITgcm-support@mitgcm.org} or browse at: |
| 26 |
``browsable'' copy of the code and a searchable database of the model |
\begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml} |
|
and site, as well as links for downloading the model and |
|
|
documentation, to data-sources and other related sites. |
|
|
|
|
|
There is also a support news group for the model that you can email at |
|
|
\texttt{support@mitgcm.org} or browse at: |
|
| 27 |
\begin{verbatim} |
\begin{verbatim} |
| 28 |
news://mitgcm.org/mitgcm.support |
http://mitgcm.org/mailman/listinfo/mitgcm-support/ |
| 29 |
|
http://mitgcm.org/pipermail/mitgcm-support/ |
| 30 |
\end{verbatim} |
\end{verbatim} |
| 31 |
A mail to the email list will reach all the developers and be archived |
\begin{rawhtml} </A> \end{rawhtml} |
|
on the newsgroup. A users email list will be established at some time |
|
|
in the future. |
|
| 32 |
|
|
| 33 |
\section{Obtaining the code} |
\section{Obtaining the code} |
| 34 |
\label{sect:obtainingCode} |
\label{sect:obtainingCode} |
| 35 |
|
\begin{rawhtml} |
| 36 |
|
<!-- CMIREDIR:obtainingCode: --> |
| 37 |
|
\end{rawhtml} |
| 38 |
|
|
| 39 |
MITgcm can be downloaded from our system by following |
MITgcm can be downloaded from our system by following |
| 40 |
the instructions below. As a courtesy we ask that you send e-mail to us at |
the instructions below. As a courtesy we ask that you send e-mail to us at |
| 41 |
\begin{rawhtml} <A href=mailto:support@mitgcm.org> \end{rawhtml} |
\begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml} |
| 42 |
support@mitgcm.org |
MITgcm-support@mitgcm.org |
| 43 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 44 |
to enable us to keep track of who's using the model and in what application. |
to enable us to keep track of who's using the model and in what application. |
| 45 |
You can download the model two ways: |
You can download the model two ways: |
| 64 |
|
|
| 65 |
\end{enumerate} |
\end{enumerate} |
| 66 |
|
|
| 67 |
|
\subsection{Method 1 - Checkout from CVS} |
| 68 |
|
\label{sect:cvs_checkout} |
| 69 |
|
|
| 70 |
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 |
| 71 |
provides an efficient and elegant way of organizing your code and keeping |
provides an efficient and elegant way of organizing your code and keeping |
| 72 |
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 |
| 73 |
download a tar file. |
download a tar file. |
| 74 |
|
|
| 75 |
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 |
| 76 |
your .cshrc or .tcshrc: |
be set within your shell. For a csh or tcsh shell, put the following |
| 77 |
\begin{verbatim} |
\begin{verbatim} |
| 78 |
% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack |
% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack |
| 79 |
\end{verbatim} |
\end{verbatim} |
| 80 |
|
in your \texttt{.cshrc} or \texttt{.tcshrc} file. For bash or sh |
| 81 |
|
shells, put: |
| 82 |
|
\begin{verbatim} |
| 83 |
|
% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
| 84 |
|
\end{verbatim} |
| 85 |
|
in your \texttt{.profile} or \texttt{.bashrc} file. |
| 86 |
|
|
| 87 |
|
|
| 88 |
To start using CVS, register with the MITgcm CVS server using command: |
To get MITgcm through CVS, first register with the MITgcm CVS server |
| 89 |
|
using command: |
| 90 |
\begin{verbatim} |
\begin{verbatim} |
| 91 |
% cvs login ( CVS password: cvsanon ) |
% cvs login ( CVS password: cvsanon ) |
| 92 |
\end{verbatim} |
\end{verbatim} |
| 93 |
You only need to do ``cvs login'' once. |
You only need to do a ``cvs login'' once. |
| 94 |
|
|
| 95 |
To obtain the sources for release1 type: |
To obtain the latest sources type: |
| 96 |
|
\begin{verbatim} |
| 97 |
|
% cvs co MITgcm |
| 98 |
|
\end{verbatim} |
| 99 |
|
or to get a specific release type: |
| 100 |
\begin{verbatim} |
\begin{verbatim} |
| 101 |
% cvs co -d directory -P -r release1 MITgcmUV |
% cvs co -P -r checkpoint52i_post MITgcm |
| 102 |
\end{verbatim} |
\end{verbatim} |
| 103 |
|
The MITgcm web site contains further directions concerning the source |
| 104 |
|
code and CVS. It also contains a web interface to our CVS archive so |
| 105 |
|
that one may easily view the state of files, revisions, and other |
| 106 |
|
development milestones: |
| 107 |
|
\begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml} |
| 108 |
|
\begin{verbatim} |
| 109 |
|
http://mitgcm.org/source_code.html |
| 110 |
|
\end{verbatim} |
| 111 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 112 |
|
|
| 113 |
This creates a directory called \textit{directory}. If \textit{directory} |
As a convenience, the MITgcm CVS server contains aliases which are |
| 114 |
exists this command updates your code based on the repository. Each |
named subsets of the codebase. These aliases can be especially |
| 115 |
directory in the source tree contains a directory \textit{CVS}. This |
helpful when used over slow internet connections or on machines with |
| 116 |
information is required by CVS to keep track of your file versions with |
restricted storage space. Table \ref{tab:cvsModules} contains a list |
| 117 |
respect to the repository. Don't edit the files in \textit{CVS}! |
of CVS aliases |
| 118 |
You can also use CVS to download code updates. More extensive |
\begin{table}[htb] |
| 119 |
information on using CVS for maintaining MITgcm code can be found |
\centering |
| 120 |
\begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml} |
\begin{tabular}[htb]{|lp{3.25in}|}\hline |
| 121 |
|
\textbf{Alias Name} & \textbf{Information (directories) Contained} \\\hline |
| 122 |
|
\texttt{MITgcm\_code} & Only the source code -- none of the verification examples. \\ |
| 123 |
|
\texttt{MITgcm\_verif\_basic} |
| 124 |
|
& Source code plus a small set of the verification examples |
| 125 |
|
(\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5}, |
| 126 |
|
\texttt{front\_relax}, and \texttt{plume\_on\_slope}). \\ |
| 127 |
|
\texttt{MITgcm\_verif\_atmos} & Source code plus all of the atmospheric examples. \\ |
| 128 |
|
\texttt{MITgcm\_verif\_ocean} & Source code plus all of the oceanic examples. \\ |
| 129 |
|
\texttt{MITgcm\_verif\_all} & Source code plus all of the |
| 130 |
|
verification examples. \\\hline |
| 131 |
|
\end{tabular} |
| 132 |
|
\caption{MITgcm CVS Modules} |
| 133 |
|
\label{tab:cvsModules} |
| 134 |
|
\end{table} |
| 135 |
|
|
| 136 |
|
The checkout process creates a directory called \texttt{MITgcm}. If |
| 137 |
|
the directory \texttt{MITgcm} exists this command updates your code |
| 138 |
|
based on the repository. Each directory in the source tree contains a |
| 139 |
|
directory \texttt{CVS}. This information is required by CVS to keep |
| 140 |
|
track of your file versions with respect to the repository. Don't edit |
| 141 |
|
the files in \texttt{CVS}! You can also use CVS to download code |
| 142 |
|
updates. More extensive information on using CVS for maintaining |
| 143 |
|
MITgcm code can be found |
| 144 |
|
\begin{rawhtml} <A href="http://mitgcm.org/usingcvstoget.html" target="idontexist"> \end{rawhtml} |
| 145 |
here |
here |
| 146 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 147 |
. |
. |
| 148 |
|
It is important to note that the CVS aliases in Table |
| 149 |
|
\ref{tab:cvsModules} cannot be used in conjunction with the CVS |
| 150 |
|
\texttt{-d DIRNAME} option. However, the \texttt{MITgcm} directories |
| 151 |
|
they create can be changed to a different name following the check-out: |
| 152 |
|
\begin{verbatim} |
| 153 |
|
% cvs co MITgcm_verif_basic |
| 154 |
|
% mv MITgcm MITgcm_verif_basic |
| 155 |
|
\end{verbatim} |
| 156 |
|
|
| 157 |
|
\subsubsection{Upgrading from an earlier version} |
| 158 |
|
|
| 159 |
|
If you already have an earlier version of the code you can ``upgrade'' |
| 160 |
|
your copy instead of downloading the entire repository again. First, |
| 161 |
|
``cd'' (change directory) to the top of your working copy: |
| 162 |
|
\begin{verbatim} |
| 163 |
|
% cd MITgcm |
| 164 |
|
\end{verbatim} |
| 165 |
|
and then issue the cvs update command such as: |
| 166 |
|
\begin{verbatim} |
| 167 |
|
% cvs -q update -r checkpoint52i_post -d -P |
| 168 |
|
\end{verbatim} |
| 169 |
|
This will update the ``tag'' to ``checkpoint52i\_post'', add any new |
| 170 |
|
directories (-d) and remove any empty directories (-P). The -q option |
| 171 |
|
means be quiet which will reduce the number of messages you'll see in |
| 172 |
|
the terminal. If you have modified the code prior to upgrading, CVS |
| 173 |
|
will try to merge your changes with the upgrades. If there is a |
| 174 |
|
conflict between your modifications and the upgrade, it will report |
| 175 |
|
that file with a ``C'' in front, e.g.: |
| 176 |
|
\begin{verbatim} |
| 177 |
|
C model/src/ini_parms.F |
| 178 |
|
\end{verbatim} |
| 179 |
|
If the list of conflicts scrolled off the screen, you can re-issue the |
| 180 |
|
cvs update command and it will report the conflicts. Conflicts are |
| 181 |
|
indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and |
| 182 |
|
``$>>>>>>>$''. For example, |
| 183 |
|
{\small |
| 184 |
|
\begin{verbatim} |
| 185 |
|
<<<<<<< ini_parms.F |
| 186 |
|
& bottomDragLinear,myOwnBottomDragCoefficient, |
| 187 |
|
======= |
| 188 |
|
& bottomDragLinear,bottomDragQuadratic, |
| 189 |
|
>>>>>>> 1.18 |
| 190 |
|
\end{verbatim} |
| 191 |
|
} |
| 192 |
|
means that you added ``myOwnBottomDragCoefficient'' to a namelist at |
| 193 |
|
the same time and place that we added ``bottomDragQuadratic''. You |
| 194 |
|
need to resolve this conflict and in this case the line should be |
| 195 |
|
changed to: |
| 196 |
|
{\small |
| 197 |
|
\begin{verbatim} |
| 198 |
|
& bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient, |
| 199 |
|
\end{verbatim} |
| 200 |
|
} |
| 201 |
|
and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted. |
| 202 |
|
Unless you are making modifications which exactly parallel |
| 203 |
|
developments we make, these types of conflicts should be rare. |
| 204 |
|
|
| 205 |
|
\paragraph*{Upgrading to the current pre-release version} |
| 206 |
|
|
| 207 |
|
We don't make a ``release'' for every little patch and bug fix in |
| 208 |
|
order to keep the frequency of upgrades to a minimum. However, if you |
| 209 |
|
have run into a problem for which ``we have already fixed in the |
| 210 |
|
latest code'' and we haven't made a ``tag'' or ``release'' since that |
| 211 |
|
patch then you'll need to get the latest code: |
| 212 |
|
\begin{verbatim} |
| 213 |
|
% cvs -q update -A -d -P |
| 214 |
|
\end{verbatim} |
| 215 |
|
Unlike, the ``check-out'' and ``update'' procedures above, there is no |
| 216 |
|
``tag'' or release name. The -A tells CVS to upgrade to the |
| 217 |
|
very latest version. As a rule, we don't recommend this since you |
| 218 |
|
might upgrade while we are in the processes of checking in the code so |
| 219 |
|
that you may only have part of a patch. Using this method of updating |
| 220 |
|
also means we can't tell what version of the code you are working |
| 221 |
|
with. So please be sure you understand what you're doing. |
| 222 |
|
|
| 223 |
|
\subsection{Method 2 - Tar file download} |
|
\paragraph*{Conventional download method} |
|
| 224 |
\label{sect:conventionalDownload} |
\label{sect:conventionalDownload} |
| 225 |
|
|
| 226 |
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 |
| 227 |
tar file from the reference web site at: |
tar file from the web site at: |
| 228 |
\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml} |
\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml} |
| 229 |
\begin{verbatim} |
\begin{verbatim} |
| 230 |
http://mitgcm.org/download/ |
http://mitgcm.org/download/ |
| 232 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 233 |
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 |
| 234 |
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 |
| 235 |
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 |
| 236 |
|
tar file does not exist, then please contact the developers through |
| 237 |
|
the |
| 238 |
|
\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 239 |
|
MITgcm-support@mitgcm.org |
| 240 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 241 |
|
mailing list. |
| 242 |
|
|
| 243 |
\section{Model and directory structure} |
\section{Model and directory structure} |
| 244 |
|
\begin{rawhtml} |
| 245 |
The ``numerical'' model is contained within a execution environment support |
<!-- CMIREDIR:directory_structure: --> |
| 246 |
wrapper. This wrapper is designed to provide a general framework for |
\end{rawhtml} |
| 247 |
grid-point models. MITgcmUV is a specific numerical model that uses the |
|
| 248 |
framework. Under this structure the model is split into execution |
The ``numerical'' model is contained within a execution environment |
| 249 |
environment support code and conventional numerical model code. The |
support wrapper. This wrapper is designed to provide a general |
| 250 |
execution environment support code is held under the \textit{eesupp} |
framework for grid-point models. MITgcmUV is a specific numerical |
| 251 |
directory. The grid point model code is held under the \textit{model} |
model that uses the framework. Under this structure the model is split |
| 252 |
directory. Code execution actually starts in the \textit{eesupp} routines |
into execution environment support code and conventional numerical |
| 253 |
and not in the \textit{model} routines. For this reason the top-level |
model code. The execution environment support code is held under the |
| 254 |
\textit{MAIN.F} is in the \textit{eesupp/src} directory. In general, |
\texttt{eesupp} directory. The grid point model code is held under the |
| 255 |
end-users should not need to worry about this level. The top-level routine |
\texttt{model} directory. Code execution actually starts in the |
| 256 |
for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F% |
\texttt{eesupp} routines and not in the \texttt{model} routines. For |
| 257 |
}. Here is a brief description of the directory structure of the model under |
this reason the top-level \texttt{MAIN.F} is in the |
| 258 |
the root tree (a detailed description is given in section 3: Code structure). |
\texttt{eesupp/src} directory. In general, end-users should not need |
| 259 |
|
to worry about this level. The top-level routine for the numerical |
| 260 |
\begin{itemize} |
part of the code is in \texttt{model/src/THE\_MODEL\_MAIN.F}. Here is |
| 261 |
\item \textit{bin}: this directory is initially empty. It is the default |
a brief description of the directory structure of the model under the |
| 262 |
directory in which to compile the code. |
root tree (a detailed description is given in section 3: Code |
| 263 |
|
structure). |
| 264 |
\item \textit{diags}: contains the code relative to time-averaged |
|
| 265 |
diagnostics. It is subdivided into two subdirectories \textit{inc} and |
\begin{itemize} |
| 266 |
\textit{src} that contain include files (*.\textit{h} files) and Fortran |
|
| 267 |
subroutines (*.\textit{F} files), respectively. |
\item \texttt{doc}: contains brief documentation notes. |
| 268 |
|
|
| 269 |
\item \textit{doc}: contains brief documentation notes. |
\item \texttt{eesupp}: contains the execution environment source code. |
| 270 |
|
Also subdivided into two subdirectories \texttt{inc} and |
| 271 |
\item \textit{eesupp}: contains the execution environment source code. Also |
\texttt{src}. |
| 272 |
subdivided into two subdirectories \textit{inc} and \textit{src}. |
|
| 273 |
|
\item \texttt{model}: this directory contains the main source code. |
| 274 |
\item \textit{exe}: this directory is initially empty. It is the default |
Also subdivided into two subdirectories \texttt{inc} and |
| 275 |
directory in which to execute the code. |
\texttt{src}. |
| 276 |
|
|
| 277 |
\item \textit{model}: this directory contains the main source code. Also |
\item \texttt{pkg}: contains the source code for the packages. Each |
| 278 |
subdivided into two subdirectories \textit{inc} and \textit{src}. |
package corresponds to a subdirectory. For example, \texttt{gmredi} |
| 279 |
|
contains the code related to the Gent-McWilliams/Redi scheme, |
| 280 |
\item \textit{pkg}: contains the source code for the packages. Each package |
\texttt{aim} the code relative to the atmospheric intermediate |
| 281 |
corresponds to a subdirectory. For example, \textit{gmredi} contains the |
physics. The packages are described in detail in chapter \ref{chap.packagesI}. |
| 282 |
code related to the Gent-McWilliams/Redi scheme, \textit{aim} the code |
|
| 283 |
relative to the atmospheric intermediate physics. The packages are described |
\item \texttt{tools}: this directory contains various useful tools. |
| 284 |
in detail in section 3. |
For example, \texttt{genmake2} is a script written in csh (C-shell) |
| 285 |
|
that should be used to generate your makefile. The directory |
| 286 |
\item \textit{tools}: this directory contains various useful tools. For |
\texttt{adjoint} contains the makefile specific to the Tangent |
| 287 |
example, \textit{genmake} is a script written in csh (C-shell) that should |
linear and Adjoint Compiler (TAMC) that generates the adjoint code. |
| 288 |
be used to generate your makefile. The directory \textit{adjoint} contains |
The latter is described in detail in part \ref{chap.ecco}. |
| 289 |
the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that |
This directory also contains the subdirectory build\_options, which |
| 290 |
generates the adjoint code. The latter is described in details in part V. |
contains the `optfiles' with the compiler options for the different |
| 291 |
|
compilers and machines that can run MITgcm. |
| 292 |
\item \textit{utils}: this directory contains various utilities. The |
|
| 293 |
subdirectory \textit{knudsen2} contains code and a makefile that |
\item \texttt{utils}: this directory contains various utilities. The |
| 294 |
compute coefficients of the polynomial approximation to the knudsen |
subdirectory \texttt{knudsen2} contains code and a makefile that |
| 295 |
formula for an ocean nonlinear equation of state. The \textit{matlab} |
compute coefficients of the polynomial approximation to the knudsen |
| 296 |
subdirectory contains matlab scripts for reading model output directly |
formula for an ocean nonlinear equation of state. The |
| 297 |
into matlab. \textit{scripts} contains C-shell post-processing |
\texttt{matlab} subdirectory contains matlab scripts for reading |
| 298 |
scripts for joining processor-based and tiled-based model output. |
model output directly into matlab. \texttt{scripts} contains C-shell |
| 299 |
|
post-processing scripts for joining processor-based and tiled-based |
| 300 |
\item \textit{verification}: this directory contains the model examples. See |
model output. The subdirectory exch2 contains the code needed for |
| 301 |
section \ref{sect:modelExamples}. |
the exch2 package to work with different combinations of domain |
| 302 |
\end{itemize} |
decompositions. |
| 303 |
|
|
| 304 |
\section{Example experiments} |
\item \texttt{verification}: this directory contains the model |
| 305 |
\label{sect:modelExamples} |
examples. See section \ref{sect:modelExamples}. |
| 306 |
|
|
| 307 |
The MITgcm distribution comes with a set of twenty-four pre-configured |
\item \texttt{jobs}: contains sample job scripts for running MITgcm. |
| 308 |
numerical experiments. Some of these examples experiments are tests of |
|
| 309 |
individual parts of the model code, but many are fully fledged numerical |
\item \texttt{lsopt}: Line search code used for optimization. |
| 310 |
simulations. A few of the examples are used for tutorial documentation |
|
| 311 |
in sections \ref{sect:eg-baro} - \ref{sect:eg-global}. The other examples |
\item \texttt{optim}: Interface between MITgcm and line search code. |
| 312 |
follow the same general structure as the tutorial examples. However, |
|
|
they only include brief instructions in a text file called {\it README}. |
|
|
The examples are located in subdirectories under |
|
|
the directory \textit{verification}. Each |
|
|
example is briefly described below. |
|
|
|
|
|
\subsection{Full list of model examples} |
|
|
|
|
|
\begin{enumerate} |
|
|
\item \textit{exp0} - single layer, ocean double gyre (barotropic with |
|
|
free-surface). This experiment is described in detail in section |
|
|
\ref{sect:eg-baro}. |
|
|
|
|
|
\item \textit{exp1} - Four layer, ocean double gyre. This experiment is described in detail in section |
|
|
\ref{sect:eg-baroc}. |
|
|
|
|
|
\item \textit{exp2} - 4x4 degree global ocean simulation with steady |
|
|
climatological forcing. This experiment is described in detail in section |
|
|
\ref{sect:eg-global}. |
|
|
|
|
|
\item \textit{exp4} - Flow over a Gaussian bump in open-water or channel |
|
|
with open boundaries. |
|
|
|
|
|
\item \textit{exp5} - Inhomogenously forced ocean convection in a doubly |
|
|
periodic box. |
|
|
|
|
|
\item \textit{front\_relax} - Relaxation of an ocean thermal front (test for |
|
|
Gent/McWilliams scheme). 2D (Y-Z). |
|
|
|
|
|
\item \textit{internal wave} - Ocean internal wave forced by open boundary |
|
|
conditions. |
|
|
|
|
|
\item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP |
|
|
scheme; 1 month integration |
|
|
|
|
|
\item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and Suarez |
|
|
'94 forcing. |
|
|
|
|
|
\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez |
|
|
'94 forcing. |
|
|
|
|
|
\item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and |
|
|
Suarez '94 forcing on the cubed sphere. |
|
|
|
|
|
\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics. Global |
|
|
Zonal Mean configuration, 1x64x5 resolution. |
|
|
|
|
|
\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric |
|
|
physics, equatorial Slice configuration. |
|
|
2D (X-Z). |
|
|
|
|
|
\item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric |
|
|
physics. 3D Equatorial Channel configuration. |
|
|
|
|
|
\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics. |
|
|
Global configuration, on latitude longitude grid with 128x64x5 grid points |
|
|
($2.8^\circ{\rm degree}$ resolution). |
|
|
|
|
|
\item \textit{adjustment.128x64x1} Barotropic adjustment |
|
|
problem on latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm degree}$ resolution). |
|
|
|
|
|
\item \textit{adjustment.cs-32x32x1} |
|
|
Barotropic adjustment |
|
|
problem on cube sphere grid with 32x32 points per face ( roughly |
|
|
$2.8^\circ{\rm degree}$ resolution). |
|
|
|
|
|
\item \textit{advect\_cs} Two-dimensional passive advection test on |
|
|
cube sphere grid. |
|
|
|
|
|
\item \textit{advect\_xy} Two-dimensional (horizontal plane) passive advection |
|
|
test on Cartesian grid. |
|
|
|
|
|
\item \textit{advect\_yz} Two-dimensional (vertical plane) passive advection test on Cartesian grid. |
|
|
|
|
|
\item \textit{carbon} Simple passive tracer experiment. Includes derivative |
|
|
calculation. Described in detail in section \ref{sect:eg-carbon-ad}. |
|
|
|
|
|
\item \textit{flt\_example} Example of using float package. |
|
|
|
|
|
\item \textit{global\_ocean.90x40x15} Global circulation with |
|
|
GM, flux boundary conditions and poles. |
|
|
|
|
|
\item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube sphere |
|
|
grid. |
|
|
|
|
|
\end{enumerate} |
|
|
|
|
|
\subsection{Directory structure of model examples} |
|
|
|
|
|
Each example directory has the following subdirectories: |
|
|
|
|
|
\begin{itemize} |
|
|
\item \textit{code}: contains the code particular to the example. At a |
|
|
minimum, this directory includes the following files: |
|
|
|
|
|
\begin{itemize} |
|
|
\item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to the |
|
|
``execution environment'' part of the code. The default version is located |
|
|
in \textit{eesupp/inc}. |
|
|
|
|
|
\item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the |
|
|
``numerical model'' part of the code. The default version is located in |
|
|
\textit{model/inc}. |
|
|
|
|
|
\item \textit{code/SIZE.h}: declares size of underlying computational grid. |
|
|
The default version is located in \textit{model/inc}. |
|
|
\end{itemize} |
|
|
|
|
|
In addition, other include files and subroutines might be present in \textit{% |
|
|
code} depending on the particular experiment. See section 2 for more details. |
|
|
|
|
|
\item \textit{input}: contains the input data files required to run the |
|
|
example. At a minimum, the \textit{input} directory contains the following |
|
|
files: |
|
|
|
|
|
\begin{itemize} |
|
|
\item \textit{input/data}: this file, written as a namelist, specifies the |
|
|
main parameters for the experiment. |
|
|
|
|
|
\item \textit{input/data.pkg}: contains parameters relative to the packages |
|
|
used in the experiment. |
|
|
|
|
|
\item \textit{input/eedata}: this file contains ``execution environment'' |
|
|
data. At present, this consists of a specification of the number of threads |
|
|
to use in $X$ and $Y$ under multithreaded execution. |
|
| 313 |
\end{itemize} |
\end{itemize} |
| 314 |
|
|
| 315 |
In addition, you will also find in this directory the forcing and topography |
\section[Building MITgcm]{Building the code} |
|
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} |
|
| 316 |
\label{sect:buildingCode} |
\label{sect:buildingCode} |
| 317 |
|
\begin{rawhtml} |
| 318 |
|
<!-- CMIREDIR:buildingCode: --> |
| 319 |
|
\end{rawhtml} |
| 320 |
|
|
| 321 |
|
To compile the code, we use the \texttt{make} program. This uses a |
| 322 |
|
file (\texttt{Makefile}) that allows us to pre-process source files, |
| 323 |
|
specify compiler and optimization options and also figures out any |
| 324 |
|
file dependencies. We supply a script (\texttt{genmake2}), described |
| 325 |
|
in section \ref{sect:genmake}, that automatically creates the |
| 326 |
|
\texttt{Makefile} for you. You then need to build the dependencies and |
| 327 |
|
compile the code. |
| 328 |
|
|
| 329 |
|
As an example, assume that you want to build and run experiment |
| 330 |
|
\texttt{verification/exp2}. The are multiple ways and places to |
| 331 |
|
actually do this but here let's build the code in |
| 332 |
|
\texttt{verification/exp2/build}: |
| 333 |
|
\begin{verbatim} |
| 334 |
|
% cd verification/exp2/build |
| 335 |
|
\end{verbatim} |
| 336 |
|
First, build the \texttt{Makefile}: |
| 337 |
|
\begin{verbatim} |
| 338 |
|
% ../../../tools/genmake2 -mods=../code |
| 339 |
|
\end{verbatim} |
| 340 |
|
The command line option tells \texttt{genmake} to override model source |
| 341 |
|
code with any files in the directory \texttt{../code/}. |
| 342 |
|
|
| 343 |
|
On many systems, the \texttt{genmake2} program will be able to |
| 344 |
|
automatically recognize the hardware, find compilers and other tools |
| 345 |
|
within the user's path (``\texttt{echo \$PATH}''), and then choose an |
| 346 |
|
appropriate set of options from the files (``optfiles'') contained in |
| 347 |
|
the \texttt{tools/build\_options} directory. Under some |
| 348 |
|
circumstances, a user may have to create a new ``optfile'' in order to |
| 349 |
|
specify the exact combination of compiler, compiler flags, libraries, |
| 350 |
|
and other options necessary to build a particular configuration of |
| 351 |
|
MITgcm. In such cases, it is generally helpful to read the existing |
| 352 |
|
``optfiles'' and mimic their syntax. |
| 353 |
|
|
| 354 |
|
Through the MITgcm-support list, the MITgcm developers are willing to |
| 355 |
|
provide help writing or modifing ``optfiles''. And we encourage users |
| 356 |
|
to post new ``optfiles'' (particularly ones for new machines or |
| 357 |
|
architectures) to the |
| 358 |
|
\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 359 |
|
MITgcm-support@mitgcm.org |
| 360 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 361 |
|
list. |
| 362 |
|
|
| 363 |
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 |
|
|
dependencies. 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 dependencies 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}: |
|
| 364 |
\begin{verbatim} |
\begin{verbatim} |
| 365 |
% ../../../tools/genmake -mods=../code |
% ../../../tools/genmake2 -mods=../code -of /path/to/optfile |
| 366 |
\end{verbatim} |
\end{verbatim} |
| 367 |
|
|
| 368 |
Next, create the dependencies: |
Once a \texttt{Makefile} has been generated, we create the |
| 369 |
|
dependencies with the command: |
| 370 |
\begin{verbatim} |
\begin{verbatim} |
| 371 |
% make depend |
% make depend |
| 372 |
\end{verbatim} |
\end{verbatim} |
| 373 |
This modifies {\em Makefile} by attaching a [long] list of files on |
This modifies the \texttt{Makefile} by attaching a (usually, long) |
| 374 |
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 |
| 375 |
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 |
| 376 |
depend} also created links from the model source to this directory. |
{\tt make depend} command also creates links from the model source to |
| 377 |
|
this directory. It is important to note that the {\tt make depend} |
| 378 |
|
stage will occasionally produce warnings or errors since the |
| 379 |
|
dependency parsing tool is unable to find all of the necessary header |
| 380 |
|
files (\textit{eg.} \texttt{netcdf.inc}). In these circumstances, it |
| 381 |
|
is usually OK to ignore the warnings/errors and proceed to the next |
| 382 |
|
step. |
| 383 |
|
|
| 384 |
Now compile the code: |
Next one can compile the code using: |
| 385 |
\begin{verbatim} |
\begin{verbatim} |
| 386 |
% make |
% make |
| 387 |
\end{verbatim} |
\end{verbatim} |
| 388 |
The {\tt make} command creates an executable called \textit{mitgcmuv}. |
The {\tt make} command creates an executable called \texttt{mitgcmuv}. |
| 389 |
|
Additional make ``targets'' are defined within the makefile to aid in |
| 390 |
|
the production of adjoint and other versions of MITgcm. On SMP |
| 391 |
|
(shared multi-processor) systems, the build process can often be sped |
| 392 |
|
up appreciably using the command: |
| 393 |
|
\begin{verbatim} |
| 394 |
|
% make -j 2 |
| 395 |
|
\end{verbatim} |
| 396 |
|
where the ``2'' can be replaced with a number that corresponds to the |
| 397 |
|
number of CPUs available. |
| 398 |
|
|
| 399 |
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 |
| 400 |
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 |
| 401 |
|
first creating links to all the input files: |
| 402 |
|
\begin{verbatim} |
| 403 |
|
ln -s ../input/* . |
| 404 |
|
\end{verbatim} |
| 405 |
|
and then calling the executable with: |
| 406 |
\begin{verbatim} |
\begin{verbatim} |
| 407 |
./mitgcmuv > output.txt |
./mitgcmuv > output.txt |
| 408 |
\end{verbatim} |
\end{verbatim} |
| 409 |
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 |
| 410 |
output.txt}. |
\texttt{output.txt}. |
|
|
|
| 411 |
|
|
| 412 |
\subsection{Building/compiling the code elsewhere} |
\subsection{Building/compiling the code elsewhere} |
| 413 |
|
|
| 416 |
convenience. You can also configure and compile the code in other |
convenience. You can also configure and compile the code in other |
| 417 |
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 |
| 418 |
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 |
| 419 |
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 |
| 420 |
|
genmake2}. |
| 421 |
|
|
| 422 |
The following sections outline some possible methods of organizing you |
The following sections outline some possible methods of organizing |
| 423 |
source and data. |
your source and data. |
| 424 |
|
|
| 425 |
\subsubsection{Building from the {\em ../code directory}} |
\subsubsection{Building from the {\em ../code directory}} |
| 426 |
|
|
| 427 |
This is just as simple as building in the {\em input/} directory: |
This is just as simple as building in the {\em input/} directory: |
| 428 |
\begin{verbatim} |
\begin{verbatim} |
| 429 |
% cd verification/exp2/code |
% cd verification/exp2/code |
| 430 |
% ../../../tools/genmake |
% ../../../tools/genmake2 |
| 431 |
% make depend |
% make depend |
| 432 |
% make |
% make |
| 433 |
\end{verbatim} |
\end{verbatim} |
| 456 |
% cd verification/exp2 |
% cd verification/exp2 |
| 457 |
% mkdir build |
% mkdir build |
| 458 |
% cd build |
% cd build |
| 459 |
% ../../../tools/genmake -mods=../code |
% ../../../tools/genmake2 -mods=../code |
| 460 |
% make depend |
% make depend |
| 461 |
% make |
% make |
| 462 |
\end{verbatim} |
\end{verbatim} |
| 478 |
% ./mitgcmuv > output.txt |
% ./mitgcmuv > output.txt |
| 479 |
\end{verbatim} |
\end{verbatim} |
| 480 |
|
|
| 481 |
\subsubsection{Building from on a scratch disk} |
\subsubsection{Building on a scratch disk} |
| 482 |
|
|
| 483 |
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 |
| 484 |
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 |
| 486 |
following commands will build the model in {\em /scratch/exp2-run1}: |
following commands will build the model in {\em /scratch/exp2-run1}: |
| 487 |
\begin{verbatim} |
\begin{verbatim} |
| 488 |
% cd /scratch/exp2-run1 |
% cd /scratch/exp2-run1 |
| 489 |
% ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code |
% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ |
| 490 |
|
-mods=~/MITgcm/verification/exp2/code |
| 491 |
% make depend |
% make depend |
| 492 |
% make |
% make |
| 493 |
\end{verbatim} |
\end{verbatim} |
| 503 |
% cd /scratch/exp2 |
% cd /scratch/exp2 |
| 504 |
% mkdir build |
% mkdir build |
| 505 |
% cd build |
% cd build |
| 506 |
% ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code |
% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ |
| 507 |
|
-mods=~/MITgcm/verification/exp2/code |
| 508 |
% make depend |
% make depend |
| 509 |
% make |
% make |
| 510 |
% cd ../ |
% cd ../ |
| 514 |
\end{verbatim} |
\end{verbatim} |
| 515 |
|
|
| 516 |
|
|
| 517 |
|
\subsection{Using \texttt{genmake2}} |
|
\subsection{\textit{genmake}} |
|
| 518 |
\label{sect:genmake} |
\label{sect:genmake} |
| 519 |
|
|
| 520 |
To compile the code, use the script \textit{genmake} located in the \textit{% |
To compile the code, first use the program \texttt{genmake2} (located |
| 521 |
tools} directory. \textit{genmake} is a script that generates the makefile. |
in the \texttt{tools} directory) to generate a Makefile. |
| 522 |
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 |
| 523 |
machines and systems. However, if it doesn't work the first time on your |
``sh''--compatible shells including bash v1, bash v2, and Bourne. |
| 524 |
platform, you might need to edit certain lines of \textit{genmake} in the |
Internally, \texttt{genmake2} determines the locations of needed |
| 525 |
section containing the setups for the different machines. The file is |
files, the compiler, compiler options, libraries, and Unix tools. It |
| 526 |
structured like this: |
relies upon a number of ``optfiles'' located in the |
| 527 |
\begin{verbatim} |
\texttt{tools/build\_options} directory. |
| 528 |
. |
|
| 529 |
. |
The purpose of the optfiles is to provide all the compilation options |
| 530 |
. |
for particular ``platforms'' (where ``platform'' roughly means the |
| 531 |
general instructions (machine independent) |
combination of the hardware and the compiler) and code configurations. |
| 532 |
. |
Given the combinations of possible compilers and library dependencies |
| 533 |
. |
({\it eg.} MPI and NetCDF) there may be numerous optfiles available |
| 534 |
. |
for a single machine. The naming scheme for the majority of the |
| 535 |
- setup machine 1 |
optfiles shipped with the code is |
| 536 |
- setup machine 2 |
\begin{center} |
| 537 |
- setup machine 3 |
{\bf OS\_HARDWARE\_COMPILER } |
| 538 |
- setup machine 4 |
\end{center} |
| 539 |
etc |
where |
| 540 |
. |
\begin{description} |
| 541 |
. |
\item[OS] is the name of the operating system (generally the |
| 542 |
. |
lower-case output of the {\tt 'uname'} command) |
| 543 |
\end{verbatim} |
\item[HARDWARE] is a string that describes the CPU type and |
| 544 |
|
corresponds to output from the {\tt 'uname -m'} command: |
| 545 |
For example, the setup corresponding to a DEC alpha machine is reproduced |
\begin{description} |
| 546 |
here: |
\item[ia32] is for ``x86'' machines such as i386, i486, i586, i686, |
| 547 |
\begin{verbatim} |
and athlon |
| 548 |
case OSF1+mpi: |
\item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2) |
| 549 |
echo "Configuring for DEC Alpha" |
\item[amd64] is AMD x86\_64 systems |
| 550 |
set CPP = ( '/usr/bin/cpp -P' ) |
\item[ppc] is for Mac PowerPC systems |
| 551 |
set DEFINES = ( ${DEFINES} '-DTARGET_DEC -DWORDLENGTH=1' ) |
\end{description} |
| 552 |
set KPP = ( 'kapf' ) |
\item[COMPILER] is the compiler name (generally, the name of the |
| 553 |
set KPPFILES = ( 'main.F' ) |
FORTRAN executable) |
| 554 |
set KFLAGS1 = ( '-scan=132 -noconc -cmp=' ) |
\end{description} |
| 555 |
set FC = ( 'f77' ) |
|
| 556 |
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 |
| 557 |
set FOPTIM = ( '-O5 -fast -tune host -inline all' ) |
usable Makefiles. However, for some machines or code configurations, |
| 558 |
set NOOPTFLAGS = ( '-O0' ) |
new ``optfiles'' must be written. To create a new optfile, it is |
| 559 |
set LIBS = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' ) |
generally best to start with one of the defaults and modify it to suit |
| 560 |
set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F') |
your needs. Like \texttt{genmake2}, the optfiles are all written |
| 561 |
set RMFILES = ( '*.p.out' ) |
using a simple ``sh''--compatible syntax. While nearly all variables |
| 562 |
breaksw |
used within \texttt{genmake2} may be specified in the optfiles, the |
| 563 |
\end{verbatim} |
critical ones that should be defined are: |
| 564 |
|
|
| 565 |
Typically, these are the lines that you might need to edit to make \textit{% |
\begin{description} |
| 566 |
genmake} work on your platform if it doesn't work the first time. \textit{% |
\item[FC] the FORTRAN compiler (executable) to use |
| 567 |
genmake} understands several options that are described here: |
\item[DEFINES] the command-line DEFINE options passed to the compiler |
| 568 |
|
\item[CPP] the C pre-processor to use |
| 569 |
\begin{itemize} |
\item[NOOPTFLAGS] options flags for special files that should not be |
| 570 |
\item -rootdir=dir |
optimized |
| 571 |
|
\end{description} |
| 572 |
indicates where the model root directory is relative to the directory where |
|
| 573 |
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'' |
| 574 |
bin} directory (which is the default compilation directory) or within the |
architecture) using the GCC (g77) compiler is |
| 575 |
\textit{verification} tree. |
\begin{verbatim} |
| 576 |
|
FC=g77 |
| 577 |
\item -mods=dir1,dir2,... |
DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4' |
| 578 |
|
CPP='cpp -traditional -P' |
| 579 |
indicates the relative or absolute paths directories where the sources |
NOOPTFLAGS='-O0' |
| 580 |
should take precedence over the default versions (located in \textit{model}, |
# For IEEE, use the "-ffloat-store" option |
| 581 |
\textit{eesupp},...). Typically, this option is used when running the |
if test "x$IEEE" = x ; then |
| 582 |
examples, see below. |
FFLAGS='-Wimplicit -Wunused -Wuninitialized' |
| 583 |
|
FOPTIM='-O3 -malign-double -funroll-loops' |
| 584 |
\item -enable=pkg1,pkg2,... |
else |
| 585 |
|
FFLAGS='-Wimplicit -Wunused -ffloat-store' |
| 586 |
enables packages source code \textit{pkg1}, \textit{pkg2},... when creating |
FOPTIM='-O0 -malign-double' |
| 587 |
the makefile. |
fi |
| 588 |
|
\end{verbatim} |
| 589 |
\item -disable=pkg1,pkg2,... |
|
| 590 |
|
If you write an optfile for an unrepresented machine or compiler, you |
| 591 |
disables packages source code \textit{pkg1}, \textit{pkg2},... when creating |
are strongly encouraged to submit the optfile to the MITgcm project |
| 592 |
the makefile. |
for inclusion. Please send the file to the |
| 593 |
|
\begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 594 |
\item -platform=machine |
\begin{center} |
| 595 |
|
MITgcm-support@mitgcm.org |
| 596 |
specifies the platform for which you want the makefile. In general, you |
\end{center} |
| 597 |
won't need this option. \textit{genmake} will select the right machine for |
\begin{rawhtml} </A> \end{rawhtml} |
| 598 |
you (the one you're working on!). However, this option is useful if you have |
mailing list. |
|
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 |
|
| 599 |
|
|
| 600 |
this is used when you want to run the model in parallel processing mode |
In addition to the optfiles, \texttt{genmake2} supports a number of |
| 601 |
under mpi (see section on parallel computation for more details). |
helpful command-line options. A complete list of these options can be |
| 602 |
|
obtained from: |
| 603 |
|
\begin{verbatim} |
| 604 |
|
% genmake2 -h |
| 605 |
|
\end{verbatim} |
| 606 |
|
|
| 607 |
|
The most important command-line options are: |
| 608 |
|
\begin{description} |
| 609 |
|
|
| 610 |
|
\item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that |
| 611 |
|
should be used for a particular build. |
| 612 |
|
|
| 613 |
|
If no "optfile" is specified (either through the command line or the |
| 614 |
|
MITGCM\_OPTFILE environment variable), genmake2 will try to make a |
| 615 |
|
reasonable guess from the list provided in {\em |
| 616 |
|
tools/build\_options}. The method used for making this guess is |
| 617 |
|
to first determine the combination of operating system and hardware |
| 618 |
|
(eg. "linux\_ia32") and then find a working FORTRAN compiler within |
| 619 |
|
the user's path. When these three items have been identified, |
| 620 |
|
genmake2 will try to find an optfile that has a matching name. |
| 621 |
|
|
| 622 |
|
\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default |
| 623 |
|
set of packages to be used. The normal order of precedence for |
| 624 |
|
packages is as follows: |
| 625 |
|
\begin{enumerate} |
| 626 |
|
\item If available, the command line (\texttt{--pdefault}) settings |
| 627 |
|
over-rule any others. |
| 628 |
|
|
| 629 |
|
\item Next, \texttt{genmake2} will look for a file named |
| 630 |
|
``\texttt{packages.conf}'' in the local directory or in any of the |
| 631 |
|
directories specified with the \texttt{--mods} option. |
| 632 |
|
|
| 633 |
|
\item Finally, if neither of the above are available, |
| 634 |
|
\texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file. |
| 635 |
|
\end{enumerate} |
| 636 |
|
|
| 637 |
|
\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file |
| 638 |
|
used for packages. |
| 639 |
|
|
| 640 |
|
If not specified, the default dependency file {\em pkg/pkg\_depend} |
| 641 |
|
is used. The syntax for this file is parsed on a line-by-line basis |
| 642 |
|
where each line containes either a comment ("\#") or a simple |
| 643 |
|
"PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol |
| 644 |
|
specifies a "must be used with" or a "must not be used with" |
| 645 |
|
relationship, respectively. If no rule is specified, then it is |
| 646 |
|
assumed that the two packages are compatible and will function |
| 647 |
|
either with or without each other. |
| 648 |
|
|
| 649 |
|
\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or |
| 650 |
|
automatic differentiation options file to be used. The file is |
| 651 |
|
analogous to the ``optfile'' defined above but it specifies |
| 652 |
|
information for the AD build process. |
| 653 |
|
|
| 654 |
|
The default file is located in {\em |
| 655 |
|
tools/adjoint\_options/adjoint\_default} and it defines the "TAF" |
| 656 |
|
and "TAMC" compilers. An alternate version is also available at |
| 657 |
|
{\em tools/adjoint\_options/adjoint\_staf} that selects the newer |
| 658 |
|
"STAF" compiler. As with any compilers, it is helpful to have their |
| 659 |
|
directories listed in your {\tt \$PATH} environment variable. |
| 660 |
|
|
| 661 |
|
\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of |
| 662 |
|
directories containing ``modifications''. These directories contain |
| 663 |
|
files with names that may (or may not) exist in the main MITgcm |
| 664 |
|
source tree but will be overridden by any identically-named sources |
| 665 |
|
within the ``MODS'' directories. |
| 666 |
|
|
| 667 |
|
The order of precedence for this "name-hiding" is as follows: |
| 668 |
|
\begin{itemize} |
| 669 |
|
\item ``MODS'' directories (in the order given) |
| 670 |
|
\item Packages either explicitly specified or provided by default |
| 671 |
|
(in the order given) |
| 672 |
|
\item Packages included due to package dependencies (in the order |
| 673 |
|
that that package dependencies are parsed) |
| 674 |
|
\item The "standard dirs" (which may have been specified by the |
| 675 |
|
``-standarddirs'' option) |
| 676 |
|
\end{itemize} |
| 677 |
|
|
| 678 |
|
\item[\texttt{--mpi}] This option enables certain MPI features (using |
| 679 |
|
CPP \texttt{\#define}s) within the code and is necessary for MPI |
| 680 |
|
builds (see Section \ref{sect:mpi-build}). |
| 681 |
|
|
| 682 |
|
\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of |
| 683 |
|
soft-links and other bugs common with the \texttt{make} versions |
| 684 |
|
provided by commercial Unix vendors, GNU \texttt{make} (sometimes |
| 685 |
|
called \texttt{gmake}) should be preferred. This option provides a |
| 686 |
|
means for specifying the make executable to be used. |
| 687 |
|
|
| 688 |
|
\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX) |
| 689 |
|
machines, the ``bash'' shell is unavailable. To run on these |
| 690 |
|
systems, \texttt{genmake2} can be invoked using an ``sh'' (that is, |
| 691 |
|
a Bourne, POSIX, or compatible) shell. The syntax in these |
| 692 |
|
circumstances is: |
| 693 |
|
\begin{center} |
| 694 |
|
\texttt{\% /bin/sh genmake2 -bash=/bin/sh [...options...]} |
| 695 |
|
\end{center} |
| 696 |
|
where \texttt{/bin/sh} can be replaced with the full path and name |
| 697 |
|
of the desired shell. |
| 698 |
|
|
| 699 |
|
\end{description} |
| 700 |
|
|
| 701 |
|
|
| 702 |
|
\subsection{Building with MPI} |
| 703 |
|
\label{sect:mpi-build} |
| 704 |
|
|
| 705 |
|
Building MITgcm to use MPI libraries can be complicated due to the |
| 706 |
|
variety of different MPI implementations available, their dependencies |
| 707 |
|
or interactions with different compilers, and their often ad-hoc |
| 708 |
|
locations within file systems. For these reasons, its generally a |
| 709 |
|
good idea to start by finding and reading the documentation for your |
| 710 |
|
machine(s) and, if necessary, seeking help from your local systems |
| 711 |
|
administrator. |
| 712 |
|
|
| 713 |
\item -jam |
The steps for building MITgcm with MPI support are: |
| 714 |
|
\begin{enumerate} |
| 715 |
|
|
| 716 |
|
\item Determine the locations of your MPI-enabled compiler and/or MPI |
| 717 |
|
libraries and put them into an options file as described in Section |
| 718 |
|
\ref{sect:genmake}. One can start with one of the examples in: |
| 719 |
|
\begin{rawhtml} <A |
| 720 |
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/"> |
| 721 |
|
\end{rawhtml} |
| 722 |
|
\begin{center} |
| 723 |
|
\texttt{MITgcm/tools/build\_options/} |
| 724 |
|
\end{center} |
| 725 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 726 |
|
such as \texttt{linux\_ia32\_g77+mpi\_cg01} or |
| 727 |
|
\texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at |
| 728 |
|
hand. You may need help from your user guide or local systems |
| 729 |
|
administrator to determine the exact location of the MPI libraries. |
| 730 |
|
If libraries are not installed, MPI implementations and related |
| 731 |
|
tools are available including: |
| 732 |
|
\begin{itemize} |
| 733 |
|
\item \begin{rawhtml} <A |
| 734 |
|
href="http://www-unix.mcs.anl.gov/mpi/mpich/"> |
| 735 |
|
\end{rawhtml} |
| 736 |
|
MPICH |
| 737 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 738 |
|
|
| 739 |
|
\item \begin{rawhtml} <A |
| 740 |
|
href="http://www.lam-mpi.org/"> |
| 741 |
|
\end{rawhtml} |
| 742 |
|
LAM/MPI |
| 743 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 744 |
|
|
| 745 |
|
\item \begin{rawhtml} <A |
| 746 |
|
href="http://www.osc.edu/~pw/mpiexec/"> |
| 747 |
|
\end{rawhtml} |
| 748 |
|
MPIexec |
| 749 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 750 |
|
\end{itemize} |
| 751 |
|
|
| 752 |
|
\item Build the code with the \texttt{genmake2} \texttt{-mpi} option |
| 753 |
|
(see Section \ref{sect:genmake}) using commands such as: |
| 754 |
|
{\footnotesize \begin{verbatim} |
| 755 |
|
% ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE |
| 756 |
|
% make depend |
| 757 |
|
% make |
| 758 |
|
\end{verbatim} } |
| 759 |
|
|
| 760 |
|
\item Run the code with the appropriate MPI ``run'' or ``exec'' |
| 761 |
|
program provided with your particular implementation of MPI. |
| 762 |
|
Typical MPI packages such as MPICH will use something like: |
| 763 |
|
\begin{verbatim} |
| 764 |
|
% mpirun -np 4 -machinefile mf ./mitgcmuv |
| 765 |
|
\end{verbatim} |
| 766 |
|
Sightly more complicated scripts may be needed for many machines |
| 767 |
|
since execution of the code may be controlled by both the MPI |
| 768 |
|
library and a job scheduling and queueing system such as PBS, |
| 769 |
|
LoadLeveller, Condor, or any of a number of similar tools. A few |
| 770 |
|
example scripts (those used for our \begin{rawhtml} <A |
| 771 |
|
href="http://mitgcm.org/testing.html"> \end{rawhtml}regular |
| 772 |
|
verification runs\begin{rawhtml} </A> \end{rawhtml}) are available |
| 773 |
|
at: |
| 774 |
|
\begin{rawhtml} <A |
| 775 |
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/"> |
| 776 |
|
\end{rawhtml} |
| 777 |
|
{\footnotesize \tt |
| 778 |
|
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ } |
| 779 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 780 |
|
|
| 781 |
this is used when you want to run the model in parallel processing mode |
\end{enumerate} |
|
under jam (see section on parallel computation for more details). |
|
|
\end{itemize} |
|
| 782 |
|
|
| 783 |
For some of the examples, there is a file called \textit{.genmakerc} in the |
An example of the above process on the MITgcm cluster (``cg01'') using |
| 784 |
\textit{input} directory that has the relevant \textit{genmake} options for |
the GNU g77 compiler and the mpich MPI library is: |
|
that particular example. In this way you don't need to type the options when |
|
|
invoking \textit{genmake}. |
|
| 785 |
|
|
| 786 |
|
{\footnotesize \begin{verbatim} |
| 787 |
|
% cd MITgcm/verification/exp5 |
| 788 |
|
% mkdir build |
| 789 |
|
% cd build |
| 790 |
|
% ../../../tools/genmake2 -mpi -mods=../code \ |
| 791 |
|
-of=../../../tools/build_options/linux_ia32_g77+mpi_cg01 |
| 792 |
|
% make depend |
| 793 |
|
% make |
| 794 |
|
% cd ../input |
| 795 |
|
% /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \ |
| 796 |
|
-machinefile mf --gm-kill 5 -v -np 2 ../build/mitgcmuv |
| 797 |
|
\end{verbatim} } |
| 798 |
|
|
| 799 |
\section{Running the model} |
\section[Running MITgcm]{Running the model in prognostic mode} |
| 800 |
\label{sect:runModel} |
\label{sect:runModel} |
| 801 |
|
\begin{rawhtml} |
| 802 |
|
<!-- CMIREDIR:runModel: --> |
| 803 |
|
\end{rawhtml} |
| 804 |
|
|
| 805 |
|
If compilation finished succesfully (section \ref{sect:buildingCode}) |
| 806 |
|
then an executable called \texttt{mitgcmuv} will now exist in the |
| 807 |
|
local directory. |
| 808 |
|
|
| 809 |
If compilation finished succesfuully (section \ref{sect:buildModel}) |
To run the model as a single process (\textit{ie.} not in parallel) |
| 810 |
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: |
|
| 811 |
\begin{verbatim} |
\begin{verbatim} |
| 812 |
% ./mitgcmuv |
% ./mitgcmuv |
| 813 |
\end{verbatim} |
\end{verbatim} |
| 817 |
your screen. This output contains details such as parameter values as |
your screen. This output contains details such as parameter values as |
| 818 |
well as diagnostics such as mean Kinetic energy, largest CFL number, |
well as diagnostics such as mean Kinetic energy, largest CFL number, |
| 819 |
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 |
| 820 |
normally re-direct the {\em stdout} stream as follows: |
normally re-direct the \texttt{stdout} stream as follows: |
| 821 |
\begin{verbatim} |
\begin{verbatim} |
| 822 |
% ./mitgcmuv > output.txt |
% ./mitgcmuv > output.txt |
| 823 |
\end{verbatim} |
\end{verbatim} |
| 824 |
|
In the event that the model encounters an error and stops, it is very |
| 825 |
For the example experiments in {\em vericication}, an example of the |
helpful to include the last few line of this \texttt{output.txt} file |
| 826 |
output is kept in {\em results/output.txt} for comparison. You can compare |
along with the (\texttt{stderr}) error message within any bug reports. |
| 827 |
your {\em output.txt} with this one to check that the set-up works. |
|
| 828 |
|
For the example experiments in \texttt{verification}, an example of the |
| 829 |
|
output is kept in \texttt{results/output.txt} for comparison. You can |
| 830 |
|
compare your \texttt{output.txt} with the corresponding one for that |
| 831 |
|
experiment to check that the set-up works. |
| 832 |
|
|
| 833 |
|
|
| 834 |
|
|
| 835 |
\subsection{Output files} |
\subsection{Output files} |
| 836 |
|
|
| 837 |
The model produces various output files. At a minimum, the instantaneous |
The model produces various output files and, when using \texttt{mnc}, |
| 838 |
``state'' of the model is written out, which is made of the following files: |
sometimes even directories. Depending upon the I/O package(s) |
| 839 |
|
selected at compile time (either \texttt{mdsio} or \texttt{mnc} or |
| 840 |
|
both as determined by \texttt{code/packages.conf}) and the run-time |
| 841 |
|
flags set (in \texttt{input/data.pkg}), the following output may |
| 842 |
|
appear. |
| 843 |
|
|
| 844 |
|
|
| 845 |
|
\subsubsection{MDSIO output files} |
| 846 |
|
|
| 847 |
|
The ``traditional'' output files are generated by the \texttt{mdsio} |
| 848 |
|
package. At a minimum, the instantaneous ``state'' of the model is |
| 849 |
|
written out, which is made of the following files: |
| 850 |
|
|
| 851 |
\begin{itemize} |
\begin{itemize} |
| 852 |
\item \textit{U.00000nIter} - zonal component of velocity field (m/s and $> |
\item \texttt{U.00000nIter} - zonal component of velocity field (m/s |
| 853 |
0 $ eastward). |
and positive eastward). |
| 854 |
|
|
| 855 |
\item \textit{V.00000nIter} - meridional component of velocity field (m/s |
\item \texttt{V.00000nIter} - meridional component of velocity field |
| 856 |
and $> 0$ northward). |
(m/s and positive northward). |
| 857 |
|
|
| 858 |
\item \textit{W.00000nIter} - vertical component of velocity field (ocean: |
\item \texttt{W.00000nIter} - vertical component of velocity field |
| 859 |
m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure |
(ocean: m/s and positive upward, atmosphere: Pa/s and positive |
| 860 |
i.e. downward). |
towards increasing pressure i.e. downward). |
| 861 |
|
|
| 862 |
\item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C, |
\item \texttt{T.00000nIter} - potential temperature (ocean: |
| 863 |
atmosphere: $^{0}$K). |
$^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$). |
| 864 |
|
|
| 865 |
\item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor |
\item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water |
| 866 |
(g/kg). |
vapor (g/kg). |
| 867 |
|
|
| 868 |
\item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere: |
\item \texttt{Eta.00000nIter} - ocean: surface elevation (m), |
| 869 |
surface pressure anomaly (Pa). |
atmosphere: surface pressure anomaly (Pa). |
| 870 |
\end{itemize} |
\end{itemize} |
| 871 |
|
|
| 872 |
The chain \textit{00000nIter} consists of ten figures that specify the |
The chain \texttt{00000nIter} consists of ten figures that specify the |
| 873 |
iteration number at which the output is written out. For example, \textit{% |
iteration number at which the output is written out. For example, |
| 874 |
U.0000000300} is the zonal velocity at iteration 300. |
\texttt{U.0000000300} is the zonal velocity at iteration 300. |
| 875 |
|
|
| 876 |
In addition, a ``pickup'' or ``checkpoint'' file called: |
In addition, a ``pickup'' or ``checkpoint'' file called: |
| 877 |
|
|
| 878 |
\begin{itemize} |
\begin{itemize} |
| 879 |
\item \textit{pickup.00000nIter} |
\item \texttt{pickup.00000nIter} |
| 880 |
\end{itemize} |
\end{itemize} |
| 881 |
|
|
| 882 |
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 |
| 884 |
there is an additional ``pickup'' file: |
there is an additional ``pickup'' file: |
| 885 |
|
|
| 886 |
\begin{itemize} |
\begin{itemize} |
| 887 |
\item \textit{pickup\_cd.00000nIter} |
\item \texttt{pickup\_cd.00000nIter} |
| 888 |
\end{itemize} |
\end{itemize} |
| 889 |
|
|
| 890 |
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 |
| 891 |
in order to restart the integration. Rolling checkpoint files are the same |
in order to restart the integration. Rolling checkpoint files are the same |
| 892 |
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 |
| 893 |
\textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be |
\texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be |
| 894 |
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 |
| 895 |
output to save disk space during long integrations. |
output to save disk space during long integrations. |
| 896 |
|
|
| 897 |
|
\subsubsection{MNC output files} |
| 898 |
|
|
| 899 |
|
Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output |
| 900 |
|
is usually (though not necessarily) placed within a subdirectory with |
| 901 |
|
a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}. |
| 902 |
|
|
| 903 |
\subsection{Looking at the output} |
\subsection{Looking at the output} |
| 904 |
|
|
| 905 |
All the model data are written according to a ``meta/data'' file format. |
The ``traditional'' or mdsio model data are written according to a |
| 906 |
Each variable is associated with two files with suffix names \textit{.data} |
``meta/data'' file format. Each variable is associated with two files |
| 907 |
and \textit{.meta}. The \textit{.data} file contains the data written in |
with suffix names \texttt{.data} and \texttt{.meta}. The |
| 908 |
binary form (big\_endian by default). The \textit{.meta} file is a |
\texttt{.data} file contains the data written in binary form |
| 909 |
``header'' file that contains information about the size and the structure |
(big\_endian by default). The \texttt{.meta} file is a ``header'' file |
| 910 |
of the \textit{.data} file. This way of organizing the output is |
that contains information about the size and the structure of the |
| 911 |
particularly useful when running multi-processors calculations. The base |
\texttt{.data} file. This way of organizing the output is particularly |
| 912 |
version of the model includes a few matlab utilities to read output files |
useful when running multi-processors calculations. The base version of |
| 913 |
written in this format. The matlab scripts are located in the directory |
the model includes a few matlab utilities to read output files written |
| 914 |
\textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads |
in this format. The matlab scripts are located in the directory |
| 915 |
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} |
| 916 |
|
reads the data. Look at the comments inside the script to see how to |
| 917 |
|
use it. |
| 918 |
|
|
| 919 |
Some examples of reading and visualizing some output in {\em Matlab}: |
Some examples of reading and visualizing some output in {\em Matlab}: |
| 920 |
\begin{verbatim} |
\begin{verbatim} |
| 931 |
>> 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 |
| 932 |
\end{verbatim} |
\end{verbatim} |
| 933 |
|
|
| 934 |
\section{Doing it yourself: customizing the code} |
Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and |
| 935 |
|
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). |
|
| 936 |
|
|
| 937 |
|
The MNC output files are all in the ``self-describing'' netCDF |
| 938 |
|
format and can thus be browsed and/or plotted using tools such as: |
| 939 |
\begin{itemize} |
\begin{itemize} |
| 940 |
\item ocean convection |
\item \texttt{ncdump} is a utility which is typically included |
| 941 |
\end{itemize} |
with every netCDF install: |
| 942 |
|
\begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml} |
| 943 |
Two options are available to parameterize ocean convection: one is to use |
\begin{verbatim} |
| 944 |
the convective adjustment scheme. In this case, you need to set the variable |
http://www.unidata.ucar.edu/packages/netcdf/ |
| 945 |
\textbf{cadjFreq}, which represents the frequency (in s) with which the |
\end{verbatim} |
| 946 |
adjustment algorithm is called, to a non-zero value (if set to a negative |
\begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF |
| 947 |
value by the user, the model will set it to the tracer time step). The other |
binaries into formatted ASCII text files. |
|
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}. |
|
| 948 |
|
|
| 949 |
\begin{itemize} |
\item \texttt{ncview} utility is a very convenient and quick way |
| 950 |
\item frequency of output |
to plot netCDF data and it runs on most OSes: |
| 951 |
|
\begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml} |
| 952 |
|
\begin{verbatim} |
| 953 |
|
http://meteora.ucsd.edu/~pierce/ncview_home_page.html |
| 954 |
|
\end{verbatim} |
| 955 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 956 |
|
|
| 957 |
|
\item MatLAB(c) and other common post-processing environments provide |
| 958 |
|
various netCDF interfaces including: |
| 959 |
|
\begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml} |
| 960 |
|
\begin{verbatim} |
| 961 |
|
http://mexcdf.sourceforge.net/ |
| 962 |
|
\end{verbatim} |
| 963 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 964 |
|
\begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml} |
| 965 |
|
\begin{verbatim} |
| 966 |
|
http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html |
| 967 |
|
\end{verbatim} |
| 968 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 969 |
\end{itemize} |
\end{itemize} |
| 970 |
|
|
|
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}). |
|
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