| 79 |
|
|
| 80 |
\end{enumerate} |
\end{enumerate} |
| 81 |
|
|
| 82 |
|
\subsection{Method 1 - Checkout from CVS} |
| 83 |
|
\label{sect:cvs_checkout} |
| 84 |
|
|
| 85 |
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 |
| 86 |
provides an efficient and elegant way of organizing your code and keeping |
provides an efficient and elegant way of organizing your code and keeping |
| 87 |
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 |
| 96 |
\begin{verbatim} |
\begin{verbatim} |
| 97 |
% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
| 98 |
\end{verbatim} |
\end{verbatim} |
| 99 |
in your .profile or .bashrc file. |
in your \texttt{.profile} or \texttt{.bashrc} file. |
| 100 |
|
|
| 101 |
|
|
| 102 |
To get MITgcm through CVS, first register with the MITgcm CVS server |
To get MITgcm through CVS, first register with the MITgcm CVS server |
| 118 |
code and CVS. It also contains a web interface to our CVS archive so |
code and CVS. It also contains a web interface to our CVS archive so |
| 119 |
that one may easily view the state of files, revisions, and other |
that one may easily view the state of files, revisions, and other |
| 120 |
development milestones: |
development milestones: |
| 121 |
\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml} |
\begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml} |
| 122 |
\begin{verbatim} |
\begin{verbatim} |
| 123 |
http://mitgcm.org/source\_code.html |
http://mitgcm.org/source_code.html |
| 124 |
\end{verbatim} |
\end{verbatim} |
| 125 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 126 |
|
|
| 127 |
|
As a convenience, the MITgcm CVS server contains aliases which are |
| 128 |
|
named subsets of the codebase. These aliases can be especially |
| 129 |
|
helpful when used over slow internet connections or on machines with |
| 130 |
|
restricted storage space. Table \ref{tab:cvsModules} contains a list |
| 131 |
|
of CVS aliases |
| 132 |
|
\begin{table}[htb] |
| 133 |
|
\centering |
| 134 |
|
\begin{tabular}[htb]{|lp{3.25in}|}\hline |
| 135 |
|
\textbf{Alias Name} & \textbf{Information (directories) Contained} \\\hline |
| 136 |
|
\texttt{MITgcm\_code} & Only the source code -- none of the verification examples. \\ |
| 137 |
|
\texttt{MITgcm\_verif\_basic} |
| 138 |
|
& Source code plus a small set of the verification examples |
| 139 |
|
(\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5}, |
| 140 |
|
\texttt{front\_relax}, and \texttt{plume\_on\_slope}). \\ |
| 141 |
|
\texttt{MITgcm\_verif\_atmos} & Source code plus all of the atmospheric examples. \\ |
| 142 |
|
\texttt{MITgcm\_verif\_ocean} & Source code plus all of the oceanic examples. \\ |
| 143 |
|
\texttt{MITgcm\_verif\_all} & Source code plus all of the |
| 144 |
|
verification examples. \\\hline |
| 145 |
|
\end{tabular} |
| 146 |
|
\caption{MITgcm CVS Modules} |
| 147 |
|
\label{tab:cvsModules} |
| 148 |
|
\end{table} |
| 149 |
|
|
| 150 |
The checkout process creates a directory called \textit{MITgcm}. If |
The checkout process creates a directory called \textit{MITgcm}. If |
| 151 |
the directory \textit{MITgcm} exists this command updates your code |
the directory \textit{MITgcm} exists this command updates your code |
| 155 |
the files in \textit{CVS}! You can also use CVS to download code |
the files in \textit{CVS}! You can also use CVS to download code |
| 156 |
updates. More extensive information on using CVS for maintaining |
updates. More extensive information on using CVS for maintaining |
| 157 |
MITgcm code can be found |
MITgcm code can be found |
| 158 |
\begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml} |
\begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml} |
| 159 |
here |
here |
| 160 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 161 |
. |
. |
| 162 |
|
It is important to note that the CVS aliases in Table |
| 163 |
|
\ref{tab:cvsModules} cannot be used in conjunction with the CVS |
| 164 |
|
\texttt{-d DIRNAME} option. However, the \texttt{MITgcm} directories |
| 165 |
|
they create can be changed to a different name following the check-out: |
| 166 |
|
\begin{verbatim} |
| 167 |
|
% cvs co MITgcm_verif_basic |
| 168 |
|
% mv MITgcm MITgcm_verif_basic |
| 169 |
|
\end{verbatim} |
| 170 |
|
|
| 171 |
|
|
| 172 |
\paragraph*{Conventional download method} |
\subsection{Method 2 - Tar file download} |
| 173 |
\label{sect:conventionalDownload} |
\label{sect:conventionalDownload} |
| 174 |
|
|
| 175 |
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 |
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 |
| 184 |
us if you should need to send us your copy of the code. If a recent |
us if you should need to send us your copy of the code. If a recent |
| 185 |
tar file does not exist, then please contact the developers through |
tar file does not exist, then please contact the developers through |
| 186 |
the MITgcm-support list. |
the |
| 187 |
|
\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 188 |
|
MITgcm-support@mitgcm.org |
| 189 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 190 |
|
mailing list. |
| 191 |
|
|
| 192 |
\paragraph*{Upgrading from an earlier version} |
\subsubsection{Upgrading from an earlier version} |
| 193 |
|
|
| 194 |
If you already have an earlier version of the code you can ``upgrade'' |
If you already have an earlier version of the code you can ``upgrade'' |
| 195 |
your copy instead of downloading the entire repository again. First, |
your copy instead of downloading the entire repository again. First, |
| 215 |
cvs update command and it will report the conflicts. Conflicts are |
cvs update command and it will report the conflicts. Conflicts are |
| 216 |
indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and |
indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and |
| 217 |
``$>>>>>>>$''. For example, |
``$>>>>>>>$''. For example, |
| 218 |
|
{\small |
| 219 |
\begin{verbatim} |
\begin{verbatim} |
| 220 |
<<<<<<< ini_parms.F |
<<<<<<< ini_parms.F |
| 221 |
& bottomDragLinear,myOwnBottomDragCoefficient, |
& bottomDragLinear,myOwnBottomDragCoefficient, |
| 223 |
& bottomDragLinear,bottomDragQuadratic, |
& bottomDragLinear,bottomDragQuadratic, |
| 224 |
>>>>>>> 1.18 |
>>>>>>> 1.18 |
| 225 |
\end{verbatim} |
\end{verbatim} |
| 226 |
|
} |
| 227 |
means that you added ``myOwnBottomDragCoefficient'' to a namelist at |
means that you added ``myOwnBottomDragCoefficient'' to a namelist at |
| 228 |
the same time and place that we added ``bottomDragQuadratic''. You |
the same time and place that we added ``bottomDragQuadratic''. You |
| 229 |
need to resolve this conflict and in this case the line should be |
need to resolve this conflict and in this case the line should be |
| 230 |
changed to: |
changed to: |
| 231 |
|
{\small |
| 232 |
\begin{verbatim} |
\begin{verbatim} |
| 233 |
& bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient, |
& bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient, |
| 234 |
\end{verbatim} |
\end{verbatim} |
| 235 |
|
} |
| 236 |
and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted. |
and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted. |
| 237 |
Unless you are making modifications which exactly parallel |
Unless you are making modifications which exactly parallel |
| 238 |
developments we make, these types of conflicts should be rare. |
developments we make, these types of conflicts should be rare. |
| 266 |
\textit{eesupp} directory. The grid point model code is held under the |
\textit{eesupp} directory. The grid point model code is held under the |
| 267 |
\textit{model} directory. Code execution actually starts in the |
\textit{model} directory. Code execution actually starts in the |
| 268 |
\textit{eesupp} routines and not in the \textit{model} routines. For |
\textit{eesupp} routines and not in the \textit{model} routines. For |
| 269 |
this reason the top-level |
this reason the top-level \textit{MAIN.F} is in the |
| 270 |
\textit{MAIN.F} is in the \textit{eesupp/src} directory. In general, |
\textit{eesupp/src} directory. In general, end-users should not need |
| 271 |
end-users should not need to worry about this level. The top-level routine |
to worry about this level. The top-level routine for the numerical |
| 272 |
for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F% |
part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is |
| 273 |
}. Here is a brief description of the directory structure of the model under |
a brief description of the directory structure of the model under the |
| 274 |
the root tree (a detailed description is given in section 3: Code structure). |
root tree (a detailed description is given in section 3: Code |
| 275 |
|
structure). |
| 276 |
|
|
| 277 |
\begin{itemize} |
\begin{itemize} |
|
\item \textit{bin}: this directory is initially empty. It is the default |
|
|
directory in which to compile the code. |
|
| 278 |
|
|
| 279 |
|
\item \textit{bin}: this directory is initially empty. It is the |
| 280 |
|
default directory in which to compile the code. |
| 281 |
|
|
| 282 |
\item \textit{diags}: contains the code relative to time-averaged |
\item \textit{diags}: contains the code relative to time-averaged |
| 283 |
diagnostics. It is subdivided into two subdirectories \textit{inc} and |
diagnostics. It is subdivided into two subdirectories \textit{inc} |
| 284 |
\textit{src} that contain include files (*.\textit{h} files) and Fortran |
and \textit{src} that contain include files (*.\textit{h} files) and |
| 285 |
subroutines (*.\textit{F} files), respectively. |
Fortran subroutines (*.\textit{F} files), respectively. |
| 286 |
|
|
| 287 |
\item \textit{doc}: contains brief documentation notes. |
\item \textit{doc}: contains brief documentation notes. |
| 288 |
|
|
| 289 |
\item \textit{eesupp}: contains the execution environment source code. Also |
\item \textit{eesupp}: contains the execution environment source code. |
| 290 |
subdivided into two subdirectories \textit{inc} and \textit{src}. |
Also subdivided into two subdirectories \textit{inc} and |
| 291 |
|
\textit{src}. |
| 292 |
\item \textit{exe}: this directory is initially empty. It is the default |
|
| 293 |
directory in which to execute the code. |
\item \textit{exe}: this directory is initially empty. It is the |
| 294 |
|
default directory in which to execute the code. |
| 295 |
\item \textit{model}: this directory contains the main source code. Also |
|
| 296 |
subdivided into two subdirectories \textit{inc} and \textit{src}. |
\item \textit{model}: this directory contains the main source code. |
| 297 |
|
Also subdivided into two subdirectories \textit{inc} and |
| 298 |
\item \textit{pkg}: contains the source code for the packages. Each package |
\textit{src}. |
| 299 |
corresponds to a subdirectory. For example, \textit{gmredi} contains the |
|
| 300 |
code related to the Gent-McWilliams/Redi scheme, \textit{aim} the code |
\item \textit{pkg}: contains the source code for the packages. Each |
| 301 |
relative to the atmospheric intermediate physics. The packages are described |
package corresponds to a subdirectory. For example, \textit{gmredi} |
| 302 |
in detail in section 3. |
contains the code related to the Gent-McWilliams/Redi scheme, |
| 303 |
|
\textit{aim} the code relative to the atmospheric intermediate |
| 304 |
\item \textit{tools}: this directory contains various useful tools. For |
physics. The packages are described in detail in section 3. |
| 305 |
example, \textit{genmake2} is a script written in csh (C-shell) that should |
|
| 306 |
be used to generate your makefile. The directory \textit{adjoint} contains |
\item \textit{tools}: this directory contains various useful tools. |
| 307 |
the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that |
For example, \textit{genmake2} is a script written in csh (C-shell) |
| 308 |
generates the adjoint code. The latter is described in details in part V. |
that should be used to generate your makefile. The directory |
| 309 |
|
\textit{adjoint} contains the makefile specific to the Tangent |
| 310 |
|
linear and Adjoint Compiler (TAMC) that generates the adjoint code. |
| 311 |
|
The latter is described in details in part V. |
| 312 |
|
|
| 313 |
\item \textit{utils}: this directory contains various utilities. The |
\item \textit{utils}: this directory contains various utilities. The |
| 314 |
subdirectory \textit{knudsen2} contains code and a makefile that |
subdirectory \textit{knudsen2} contains code and a makefile that |
| 315 |
compute coefficients of the polynomial approximation to the knudsen |
compute coefficients of the polynomial approximation to the knudsen |
| 316 |
formula for an ocean nonlinear equation of state. The \textit{matlab} |
formula for an ocean nonlinear equation of state. The |
| 317 |
subdirectory contains matlab scripts for reading model output directly |
\textit{matlab} subdirectory contains matlab scripts for reading |
| 318 |
into matlab. \textit{scripts} contains C-shell post-processing |
model output directly into matlab. \textit{scripts} contains C-shell |
| 319 |
scripts for joining processor-based and tiled-based model output. |
post-processing scripts for joining processor-based and tiled-based |
| 320 |
|
model output. |
| 321 |
|
|
| 322 |
|
\item \textit{verification}: this directory contains the model |
| 323 |
|
examples. See section \ref{sect:modelExamples}. |
| 324 |
|
|
|
\item \textit{verification}: this directory contains the model examples. See |
|
|
section \ref{sect:modelExamples}. |
|
| 325 |
\end{itemize} |
\end{itemize} |
| 326 |
|
|
| 327 |
\section{Example experiments} |
\section[MITgcm Example Experiments]{Example experiments} |
| 328 |
\label{sect:modelExamples} |
\label{sect:modelExamples} |
| 329 |
|
|
| 330 |
%% a set of twenty-four pre-configured numerical experiments |
%% a set of twenty-four pre-configured numerical experiments |
| 343 |
\subsection{Full list of model examples} |
\subsection{Full list of model examples} |
| 344 |
|
|
| 345 |
\begin{enumerate} |
\begin{enumerate} |
| 346 |
|
|
| 347 |
\item \textit{exp0} - single layer, ocean double gyre (barotropic with |
\item \textit{exp0} - single layer, ocean double gyre (barotropic with |
| 348 |
free-surface). This experiment is described in detail in section |
free-surface). This experiment is described in detail in section |
| 349 |
\ref{sect:eg-baro}. |
\ref{sect:eg-baro}. |
| 469 |
of the number of threads to use in $X$ and $Y$ under multithreaded |
of the number of threads to use in $X$ and $Y$ under multithreaded |
| 470 |
execution. |
execution. |
| 471 |
\end{itemize} |
\end{itemize} |
| 472 |
|
|
| 473 |
In addition, you will also find in this directory the forcing and |
In addition, you will also find in this directory the forcing and |
| 474 |
topography files as well as the files describing the initial state of |
topography files as well as the files describing the initial state |
| 475 |
the experiment. This varies from experiment to experiment. See |
of the experiment. This varies from experiment to experiment. See |
| 476 |
section 2 for more details. |
section 2 for more details. |
| 477 |
|
|
| 478 |
\item \textit{results}: this directory contains the output file |
\item \textit{results}: this directory contains the output file |
| 479 |
\textit{output.txt} produced by the simulation example. This file is |
\textit{output.txt} produced by the simulation example. This file is |
| 481 |
experiment. |
experiment. |
| 482 |
\end{itemize} |
\end{itemize} |
| 483 |
|
|
| 484 |
Once you have chosen the example you want to run, you are ready to compile |
Once you have chosen the example you want to run, you are ready to |
| 485 |
the code. |
compile the code. |
| 486 |
|
|
| 487 |
\section{Building the code} |
\section[Building MITgcm]{Building the code} |
| 488 |
\label{sect:buildingCode} |
\label{sect:buildingCode} |
| 489 |
|
|
| 490 |
To compile the code, we use the {\em make} program. This uses a file |
To compile the code, we use the {\em make} program. This uses a file |
| 523 |
Through the MITgcm-support list, the MITgcm developers are willing to |
Through the MITgcm-support list, the MITgcm developers are willing to |
| 524 |
provide help writing or modifing ``optfiles''. And we encourage users |
provide help writing or modifing ``optfiles''. And we encourage users |
| 525 |
to post new ``optfiles'' (particularly ones for new machines or |
to post new ``optfiles'' (particularly ones for new machines or |
| 526 |
architectures) to the MITgcm-support list. |
architectures) to the |
| 527 |
|
\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 528 |
|
MITgcm-support@mitgcm.org |
| 529 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 530 |
|
list. |
| 531 |
|
|
| 532 |
To specify an optfile to {\em genmake2}, the syntax is: |
To specify an optfile to {\em genmake2}, the syntax is: |
| 533 |
\begin{verbatim} |
\begin{verbatim} |
| 666 |
\end{verbatim} |
\end{verbatim} |
| 667 |
|
|
| 668 |
|
|
| 669 |
|
\subsection{Using \texttt{genmake2}} |
|
\subsection{Using \textit{genmake2}} |
|
| 670 |
\label{sect:genmake} |
\label{sect:genmake} |
| 671 |
|
|
| 672 |
To compile the code, first use the program \texttt{genmake2} (located |
To compile the code, first use the program \texttt{genmake2} (located |
| 673 |
in the \textit{tools} directory) to generate a Makefile. |
in the \texttt{tools} directory) to generate a Makefile. |
| 674 |
\texttt{genmake2} is a shell script written to work with all |
\texttt{genmake2} is a shell script written to work with all |
| 675 |
``sh''--compatible shells including bash v1, bash v2, and Bourne. |
``sh''--compatible shells including bash v1, bash v2, and Bourne. |
| 676 |
Internally, \texttt{genmake2} determines the locations of needed |
Internally, \texttt{genmake2} determines the locations of needed |
| 677 |
files, the compiler, compiler options, libraries, and Unix tools. It |
files, the compiler, compiler options, libraries, and Unix tools. It |
| 678 |
relies upon a number of ``optfiles'' located in the {\em |
relies upon a number of ``optfiles'' located in the |
| 679 |
tools/build\_options} directory. |
\texttt{tools/build\_options} directory. |
| 680 |
|
|
| 681 |
The purpose of the optfiles is to provide all the compilation options |
The purpose of the optfiles is to provide all the compilation options |
| 682 |
for particular ``platforms'' (where ``platform'' roughly means the |
for particular ``platforms'' (where ``platform'' roughly means the |
| 759 |
The most important command-line options are: |
The most important command-line options are: |
| 760 |
\begin{description} |
\begin{description} |
| 761 |
|
|
| 762 |
\item[--optfile=/PATH/FILENAME] specifies the optfile that should be |
\item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that |
| 763 |
used for a particular build. |
should be used for a particular build. |
| 764 |
|
|
| 765 |
If no "optfile" is specified (either through the command line or the |
If no "optfile" is specified (either through the command line or the |
| 766 |
MITGCM\_OPTFILE environment variable), genmake2 will try to make a |
MITGCM\_OPTFILE environment variable), genmake2 will try to make a |
| 771 |
the user's path. When these three items have been identified, |
the user's path. When these three items have been identified, |
| 772 |
genmake2 will try to find an optfile that has a matching name. |
genmake2 will try to find an optfile that has a matching name. |
| 773 |
|
|
| 774 |
\item[--pdepend=/PATH/FILENAME] specifies the dependency file used for |
\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default |
| 775 |
packages. |
set of packages to be used. The normal order of precedence for |
| 776 |
|
packages is as follows: |
| 777 |
|
\begin{enumerate} |
| 778 |
|
\item If available, the command line (\texttt{--pdefault}) settings |
| 779 |
|
over-rule any others. |
| 780 |
|
|
| 781 |
|
\item Next, \texttt{genmake2} will look for a file named |
| 782 |
|
``\texttt{packages.conf}'' in the local directory or in any of the |
| 783 |
|
directories specified with the \texttt{--mods} option. |
| 784 |
|
|
| 785 |
|
\item Finally, if neither of the above are available, |
| 786 |
|
\texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file. |
| 787 |
|
\end{enumerate} |
| 788 |
|
|
| 789 |
|
\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file |
| 790 |
|
used for packages. |
| 791 |
|
|
| 792 |
If not specified, the default dependency file {\em pkg/pkg\_depend} |
If not specified, the default dependency file {\em pkg/pkg\_depend} |
| 793 |
is used. The syntax for this file is parsed on a line-by-line basis |
is used. The syntax for this file is parsed on a line-by-line basis |
| 798 |
assumed that the two packages are compatible and will function |
assumed that the two packages are compatible and will function |
| 799 |
either with or without each other. |
either with or without each other. |
| 800 |
|
|
| 801 |
\item[--pdefault='PKG1 PKG2 PKG3 ...'] specifies the default set of |
\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or |
| 802 |
packages to be used. |
automatic differentiation options file to be used. The file is |
| 803 |
|
analogous to the ``optfile'' defined above but it specifies |
| 804 |
If not set, the default package list will be read from {\em |
information for the AD build process. |
|
pkg/pkg\_default} |
|
|
|
|
|
\item[--adof=/path/to/file] specifies the "adjoint" or automatic |
|
|
differentiation options file to be used. The file is analogous to |
|
|
the ``optfile'' defined above but it specifies information for the |
|
|
AD build process. |
|
| 805 |
|
|
| 806 |
The default file is located in {\em |
The default file is located in {\em |
| 807 |
tools/adjoint\_options/adjoint\_default} and it defines the "TAF" |
tools/adjoint\_options/adjoint\_default} and it defines the "TAF" |
| 810 |
"STAF" compiler. As with any compilers, it is helpful to have their |
"STAF" compiler. As with any compilers, it is helpful to have their |
| 811 |
directories listed in your {\tt \$PATH} environment variable. |
directories listed in your {\tt \$PATH} environment variable. |
| 812 |
|
|
| 813 |
\item[--mods='DIR1 DIR2 DIR3 ...'] specifies a list of directories |
\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of |
| 814 |
containing ``modifications''. These directories contain files with |
directories containing ``modifications''. These directories contain |
| 815 |
names that may (or may not) exist in the main MITgcm source tree but |
files with names that may (or may not) exist in the main MITgcm |
| 816 |
will be overridden by any identically-named sources within the |
source tree but will be overridden by any identically-named sources |
| 817 |
``MODS'' directories. |
within the ``MODS'' directories. |
| 818 |
|
|
| 819 |
The order of precedence for this "name-hiding" is as follows: |
The order of precedence for this "name-hiding" is as follows: |
| 820 |
\begin{itemize} |
\begin{itemize} |
| 827 |
``-standarddirs'' option) |
``-standarddirs'' option) |
| 828 |
\end{itemize} |
\end{itemize} |
| 829 |
|
|
| 830 |
\item[--make=/path/to/gmake] Due to the poor handling of soft-links and |
\item[\texttt{--mpi}] This option enables certain MPI features (using |
| 831 |
other bugs common with the \texttt{make} versions provided by |
CPP \texttt{\#define}s) within the code and is necessary for MPI |
| 832 |
commercial Unix vendors, GNU \texttt{make} (sometimes called |
builds (see Section \ref{sect:mpi-build}). |
| 833 |
\texttt{gmake}) should be preferred. This option provides a means |
|
| 834 |
for specifying the make executable to be used. |
\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of |
| 835 |
|
soft-links and other bugs common with the \texttt{make} versions |
| 836 |
|
provided by commercial Unix vendors, GNU \texttt{make} (sometimes |
| 837 |
|
called \texttt{gmake}) should be preferred. This option provides a |
| 838 |
|
means for specifying the make executable to be used. |
| 839 |
|
|
| 840 |
|
\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX) |
| 841 |
|
machines, the ``bash'' shell is unavailable. To run on these |
| 842 |
|
systems, \texttt{genmake2} can be invoked using an ``sh'' (that is, |
| 843 |
|
a Bourne, POSIX, or compatible) shell. The syntax in these |
| 844 |
|
circumstances is: |
| 845 |
|
\begin{center} |
| 846 |
|
\texttt{\% /bin/sh genmake2 -bash=/bin/sh [...options...]} |
| 847 |
|
\end{center} |
| 848 |
|
where \texttt{/bin/sh} can be replaced with the full path and name |
| 849 |
|
of the desired shell. |
| 850 |
|
|
| 851 |
\end{description} |
\end{description} |
| 852 |
|
|
| 853 |
|
|
| 854 |
|
\subsection{Building with MPI} |
| 855 |
|
\label{sect:mpi-build} |
| 856 |
|
|
| 857 |
|
Building MITgcm to use MPI libraries can be complicated due to the |
| 858 |
|
variety of different MPI implementations available, their dependencies |
| 859 |
|
or interactions with different compilers, and their often ad-hoc |
| 860 |
|
locations within file systems. For these reasons, its generally a |
| 861 |
|
good idea to start by finding and reading the documentation for your |
| 862 |
|
machine(s) and, if necessary, seeking help from your local systems |
| 863 |
|
administrator. |
| 864 |
|
|
| 865 |
|
The steps for building MITgcm with MPI support are: |
| 866 |
|
\begin{enumerate} |
| 867 |
|
|
| 868 |
|
\item Determine the locations of your MPI-enabled compiler and/or MPI |
| 869 |
|
libraries and put them into an options file as described in Section |
| 870 |
|
\ref{sect:genmake}. One can start with one of the examples in: |
| 871 |
|
\begin{rawhtml} <A |
| 872 |
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/"> |
| 873 |
|
\end{rawhtml} |
| 874 |
|
\begin{center} |
| 875 |
|
\texttt{MITgcm/tools/build\_options/} |
| 876 |
|
\end{center} |
| 877 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 878 |
|
such as \texttt{linux\_ia32\_g77+mpi\_cg01} or |
| 879 |
|
\texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at |
| 880 |
|
hand. You may need help from your user guide or local systems |
| 881 |
|
administrator to determine the exact location of the MPI libraries. |
| 882 |
|
If libraries are not installed, MPI implementations and related |
| 883 |
|
tools are available including: |
| 884 |
|
\begin{itemize} |
| 885 |
|
\item \begin{rawhtml} <A |
| 886 |
|
href="http://www-unix.mcs.anl.gov/mpi/mpich/"> |
| 887 |
|
\end{rawhtml} |
| 888 |
|
MPICH |
| 889 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 890 |
|
|
| 891 |
|
\item \begin{rawhtml} <A |
| 892 |
|
href="http://www.lam-mpi.org/"> |
| 893 |
|
\end{rawhtml} |
| 894 |
|
LAM/MPI |
| 895 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 896 |
|
|
| 897 |
|
\item \begin{rawhtml} <A |
| 898 |
|
href="http://www.osc.edu/~pw/mpiexec/"> |
| 899 |
|
\end{rawhtml} |
| 900 |
|
MPIexec |
| 901 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 902 |
|
\end{itemize} |
| 903 |
|
|
| 904 |
|
\item Build the code with the \texttt{genmake2} \texttt{-mpi} option |
| 905 |
|
(see Section \ref{sect:genmake}) using commands such as: |
| 906 |
|
{\footnotesize \begin{verbatim} |
| 907 |
|
% ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE |
| 908 |
|
% make depend |
| 909 |
|
% make |
| 910 |
|
\end{verbatim} } |
| 911 |
|
|
| 912 |
|
\item Run the code with the appropriate MPI ``run'' or ``exec'' |
| 913 |
|
program provided with your particular implementation of MPI. |
| 914 |
|
Typical MPI packages such as MPICH will use something like: |
| 915 |
|
\begin{verbatim} |
| 916 |
|
% mpirun -np 4 -machinefile mf ./mitgcmuv |
| 917 |
|
\end{verbatim} |
| 918 |
|
Sightly more complicated scripts may be needed for many machines |
| 919 |
|
since execution of the code may be controlled by both the MPI |
| 920 |
|
library and a job scheduling and queueing system such as PBS, |
| 921 |
|
LoadLeveller, Condor, or any of a number of similar tools. A few |
| 922 |
|
example scripts (those used for our \begin{rawhtml} <A |
| 923 |
|
href="http://mitgcm.org/testing.html"> \end{rawhtml}regular |
| 924 |
|
verification runs\begin{rawhtml} </A> \end{rawhtml}) are available |
| 925 |
|
at: |
| 926 |
|
\begin{rawhtml} <A |
| 927 |
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/"> |
| 928 |
|
\end{rawhtml} |
| 929 |
|
{\footnotesize \tt |
| 930 |
|
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ } |
| 931 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 932 |
|
|
| 933 |
|
\end{enumerate} |
| 934 |
|
|
| 935 |
\section{Running the model} |
An example of the above process on the MITgcm cluster (``cg01'') using |
| 936 |
|
the GNU g77 compiler and the mpich MPI library is: |
| 937 |
|
|
| 938 |
|
{\footnotesize \begin{verbatim} |
| 939 |
|
% cd MITgcm/verification/exp5 |
| 940 |
|
% mkdir build |
| 941 |
|
% cd build |
| 942 |
|
% ../../../tools/genmake2 -mpi -mods=../code \ |
| 943 |
|
-of=../../../tools/build_options/linux_ia32_g77+mpi_cg01 |
| 944 |
|
% make depend |
| 945 |
|
% make |
| 946 |
|
% cd ../input |
| 947 |
|
% /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \ |
| 948 |
|
-machinefile mf --gm-kill 5 -v -np 2 ../build/mitgcmuv |
| 949 |
|
\end{verbatim} } |
| 950 |
|
|
| 951 |
|
|
| 952 |
|
|
| 953 |
|
\section[Running MITgcm]{Running the model in prognostic mode} |
| 954 |
\label{sect:runModel} |
\label{sect:runModel} |
| 955 |
|
|
| 956 |
If compilation finished succesfuully (section \ref{sect:buildModel}) |
If compilation finished succesfuully (section \ref{sect:buildingCode}) |
| 957 |
then an executable called {\em mitgcmuv} will now exist in the local |
then an executable called \texttt{mitgcmuv} will now exist in the |
| 958 |
directory. |
local directory. |
| 959 |
|
|
| 960 |
To run the model as a single process (ie. not in parallel) simply |
To run the model as a single process (ie. not in parallel) simply |
| 961 |
type: |
type: |
| 973 |
% ./mitgcmuv > output.txt |
% ./mitgcmuv > output.txt |
| 974 |
\end{verbatim} |
\end{verbatim} |
| 975 |
|
|
| 976 |
For the example experiments in {\em vericication}, an example of the |
For the example experiments in {\em verification}, an example of the |
| 977 |
output is kept in {\em results/output.txt} for comparison. You can compare |
output is kept in {\em results/output.txt} for comparison. You can compare |
| 978 |
your {\em output.txt} with this one to check that the set-up works. |
your {\em output.txt} with this one to check that the set-up works. |
| 979 |
|
|
| 1059 |
>> 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 |
| 1060 |
\end{verbatim} |
\end{verbatim} |
| 1061 |
|
|
|
\section{Doing it yourself: customizing the code} |
|
|
|
|
|
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} 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} 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} and \textbf{eosType}. |
|
|
\textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and |
|
|
needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. |
|
|
In this case, \textbf{eosType} must be set to '\texttt{IDEALGAS}'. |
|
|
For the ocean, two forms of the equation of state are available: |
|
|
linear (set \textbf{eosType} 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} (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). |
|
|
|
|
|
There there are also higher polynomials for the equation of state: |
|
|
\begin{description} |
|
|
\item['\texttt{UNESCO}':] The UNESCO equation of state formula of |
|
|
Fofonoff and Millard \cite{fofonoff83}. This equation of state |
|
|
assumes in-situ temperature, which is not a model variable; \emph{its use |
|
|
is therefore discouraged, and it is only listed for completeness}. |
|
|
\item['\texttt{JMD95Z}':] A modified UNESCO formula by Jackett and |
|
|
McDougall \cite{jackett95}, which uses the model variable potential |
|
|
temperature as input. The '\texttt{Z}' indicates that this equation |
|
|
of state uses a horizontally and temporally constant pressure |
|
|
$p_{0}=-g\rho_{0}z$. |
|
|
\item['\texttt{JMD95P}':] A modified UNESCO formula by Jackett and |
|
|
McDougall \cite{jackett95}, which uses the model variable potential |
|
|
temperature as input. The '\texttt{P}' indicates that this equation |
|
|
of state uses the actual hydrostatic pressure of the last time |
|
|
step. Lagging the pressure in this way requires an additional pickup |
|
|
file for restarts. |
|
|
\item['\texttt{MDJWF}':] The new, more accurate and less expensive |
|
|
equation of state by McDougall et~al. \cite{mcdougall03}. It also |
|
|
requires lagging the pressure and therefore an additional pickup |
|
|
file for restarts. |
|
|
\end{description} |
|
|
For none of these options an reference profile of temperature or |
|
|
salinity is required. |
|
|
|
|
|
\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). |
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\begin{itemize} |
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\item forcing |
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\end{itemize} |
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This section only applies to the ocean. You need to generate wind-stress |
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data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{% |
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meridWindFile }corresponding to the zonal and meridional components of the |
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wind stress, respectively (if you want the stress to be along the direction |
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of only one of the model horizontal axes, you only need to generate one |
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file). The format of the files is similar to the bathymetry file. The zonal |
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(meridional) stress data are assumed to be in Pa and located at U-points |
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(V-points). As for the bathymetry, the precision with which to read the |
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binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } |
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See the matlab program \textit{gendata.m }in the \textit{input }directories |
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under \textit{verification }to see how simple analytical wind forcing data |
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are generated for the case study experiments. |
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There is also the possibility of prescribing time-dependent periodic |
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forcing. To do this, concatenate the successive time records into a single |
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file (for each stress component) ordered in a (x, y, t) fashion and set the |
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following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.', |
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\textbf{externForcingPeriod }to the period (in s) of which the forcing |
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varies (typically 1 month), and \textbf{externForcingCycle }to the repeat |
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time (in s) of the forcing (typically 1 year -- note: \textbf{% |
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externForcingCycle }must be a multiple of \textbf{externForcingPeriod}). |
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With these variables set up, the model will interpolate the forcing linearly |
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at each iteration. |
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\begin{itemize} |
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\item dissipation |
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\end{itemize} |
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The lateral eddy viscosity coefficient is specified through the variable |
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\textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity |
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coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$% |
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^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) |
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for the atmosphere. The vertical diffusive fluxes can be computed implicitly |
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by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}% |
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.'. In addition, biharmonic mixing can be added as well through the variable |
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\textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid, |
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you might also need to set the variable \textbf{cosPower} which is set to 0 |
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by default and which represents the power of cosine of latitude to multiply |
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viscosity. Slip or no-slip conditions at lateral and bottom boundaries are |
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specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }% |
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and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip |
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boundary conditions are applied. If no-slip boundary conditions are applied |
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at the bottom, a bottom drag can be applied as well. Two forms are |
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available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$% |
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^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{% |
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\ }in m$^{-1}$). |
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The Fourier and Shapiro filters are described elsewhere. |
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\begin{itemize} |
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\item C-D scheme |
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\end{itemize} |
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If you run at a sufficiently coarse resolution, you will need the C-D scheme |
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for the computation of the Coriolis terms. The variable\textbf{\ tauCD}, |
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which represents the C-D scheme coupling timescale (in s) needs to be set. |
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\begin{itemize} |
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\item calculation of pressure/geopotential |
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\end{itemize} |
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First, to run a non-hydrostatic ocean simulation, set the logical variable |
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\textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure field is then |
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inverted through a 3D elliptic equation. (Note: this capability is not |
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available for the atmosphere yet.) By default, a hydrostatic simulation is |
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assumed and a 2D elliptic equation is used to invert the pressure field. The |
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parameters controlling the behaviour of the elliptic solvers are the |
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variables \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual }% |
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for the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{% |
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cg3dTargetResidual }for the 3D case. You probably won't need to alter the |
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default values (are we sure of this?). |
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For the calculation of the surface pressure (for the ocean) or surface |
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geopotential (for the atmosphere) you need to set the logical variables |
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\textbf{rigidLid} and \textbf{implicitFreeSurface}\textit{\ }(set one to '.% |
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\texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you |
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want to deal with the ocean upper or atmosphere lower boundary). |
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\subsection{Tracer equations} |
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This section covers the tracer equations i.e. the potential temperature |
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equation and the salinity (for the ocean) or specific humidity (for the |
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atmosphere) equation. As for the momentum equations, we only describe for |
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now the parameters that you are likely to change. The logical variables |
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\textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{% |
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tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off |
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terms in the temperature equation (same thing for salinity or specific |
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humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{% |
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saltAdvection}\textit{\ }etc). These variables are all assumed here to be |
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set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a |
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precise definition. |
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\begin{itemize} |
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\item initialization |
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\end{itemize} |
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The initial tracer data can be contained in the binary files \textbf{% |
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hydrogThetaFile }and \textbf{hydrogSaltFile}. These files should contain 3D |
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data ordered in an (x, y, r) fashion with k=1 as the first vertical level. |
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If no file names are provided, the tracers are then initialized with the |
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values of \textbf{tRef }and \textbf{sRef }mentioned above (in the equation |
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of state section). In this case, the initial tracer data are uniform in x |
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and y for each depth level. |
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\begin{itemize} |
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|
\item forcing |
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\end{itemize} |
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This part is more relevant for the ocean, the procedure for the atmosphere |
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not being completely stabilized at the moment. |
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A combination of fluxes data and relaxation terms can be used for driving |
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the tracer equations. \ For potential temperature, heat flux data (in W/m$% |
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|
^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }% |
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|
Alternatively or in addition, the forcing can be specified through a |
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|
relaxation term. The SST data to which the model surface temperatures are |
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|
restored to are supposed to be stored in the 2D binary file \textbf{% |
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thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient |
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|
is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The |
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|
same procedure applies for salinity with the variable names \textbf{EmPmRfile% |
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|
}\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}% |
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\textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data |
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|
files and relaxation time scale coefficient (in s), respectively. Also for |
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|
salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural |
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boundary conditions are applied i.e. when computing the surface salinity |
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|
tendency, the freshwater flux is multiplied by the model surface salinity |
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|
instead of a constant salinity value. |
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As for the other input files, the precision with which to read the data is |
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|
controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic |
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|
forcing can be applied as well following the same procedure used for the |
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|
wind forcing data (see above). |
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\begin{itemize} |
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|
\item dissipation |
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|
\end{itemize} |
|
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|
Lateral eddy diffusivities for temperature and salinity/specific humidity |
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|
are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }% |
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|
(in m$^{2}$/s). Vertical eddy diffusivities are specified through the |
|
|
variables \textbf{diffKzT }and \textbf{diffKzS }(in m$^{2}$/s) for the ocean |
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|
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). |
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|
\begin{itemize} |
|
|
\item ocean convection |
|
|
\end{itemize} |
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|
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 |
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|
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 |
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|
\textbf{ivdc\_kappa }can not both have non-zero value. |
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\subsection{Simulation controls} |
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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). |
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|
\begin{itemize} |
|
|
\item run duration |
|
|
\end{itemize} |
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|
|
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}. |
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|
|
\begin{itemize} |
|
|
\item frequency of output |
|
|
\end{itemize} |
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|
|
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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%%% Local Variables: |
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%%% mode: latex |
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|
%%% TeX-master: t |
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%%% End: |
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