| 17 |
|
|
| 18 |
\section{Where to find information} |
\section{Where to find information} |
| 19 |
\label{sect:whereToFindInfo} |
\label{sect:whereToFindInfo} |
| 20 |
|
\begin{rawhtml} |
| 21 |
|
<!-- CMIREDIR:whereToFindInfo: --> |
| 22 |
|
\end{rawhtml} |
| 23 |
|
|
| 24 |
A web site is maintained for release 2 (``Pelican'') of MITgcm: |
A web site is maintained for release 2 (``Pelican'') of MITgcm: |
| 25 |
\begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml} |
\begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml} |
| 53 |
|
|
| 54 |
\section{Obtaining the code} |
\section{Obtaining the code} |
| 55 |
\label{sect:obtainingCode} |
\label{sect:obtainingCode} |
| 56 |
|
\begin{rawhtml} |
| 57 |
|
<!-- CMIREDIR:obtainingCode: --> |
| 58 |
|
\end{rawhtml} |
| 59 |
|
|
| 60 |
MITgcm can be downloaded from our system by following |
MITgcm can be downloaded from our system by following |
| 61 |
the instructions below. As a courtesy we ask that you send e-mail to us at |
the instructions below. As a courtesy we ask that you send e-mail to us at |
| 85 |
|
|
| 86 |
\end{enumerate} |
\end{enumerate} |
| 87 |
|
|
| 88 |
\subsubsection{Checkout from CVS} |
\subsection{Method 1 - Checkout from CVS} |
| 89 |
\label{sect:cvs_checkout} |
\label{sect:cvs_checkout} |
| 90 |
|
|
| 91 |
If CVS is available on your system, we strongly encourage you to use it. CVS |
If CVS is available on your system, we strongly encourage you to use it. CVS |
| 98 |
\begin{verbatim} |
\begin{verbatim} |
| 99 |
% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack |
% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack |
| 100 |
\end{verbatim} |
\end{verbatim} |
| 101 |
in your .cshrc or .tcshrc file. For bash or sh shells, put: |
in your \texttt{.cshrc} or \texttt{.tcshrc} file. For bash or sh |
| 102 |
|
shells, put: |
| 103 |
\begin{verbatim} |
\begin{verbatim} |
| 104 |
% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
| 105 |
\end{verbatim} |
\end{verbatim} |
| 125 |
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 |
| 126 |
that one may easily view the state of files, revisions, and other |
that one may easily view the state of files, revisions, and other |
| 127 |
development milestones: |
development milestones: |
| 128 |
\begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml} |
\begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml} |
| 129 |
\begin{verbatim} |
\begin{verbatim} |
| 130 |
http://mitgcm.org/source_code.html |
http://mitgcm.org/source_code.html |
| 131 |
\end{verbatim} |
\end{verbatim} |
| 154 |
\label{tab:cvsModules} |
\label{tab:cvsModules} |
| 155 |
\end{table} |
\end{table} |
| 156 |
|
|
| 157 |
The checkout process creates a directory called \textit{MITgcm}. If |
The checkout process creates a directory called \texttt{MITgcm}. If |
| 158 |
the directory \textit{MITgcm} exists this command updates your code |
the directory \texttt{MITgcm} exists this command updates your code |
| 159 |
based on the repository. Each directory in the source tree contains a |
based on the repository. Each directory in the source tree contains a |
| 160 |
directory \textit{CVS}. This information is required by CVS to keep |
directory \texttt{CVS}. This information is required by CVS to keep |
| 161 |
track of your file versions with respect to the repository. Don't edit |
track of your file versions with respect to the repository. Don't edit |
| 162 |
the files in \textit{CVS}! You can also use CVS to download code |
the files in \texttt{CVS}! You can also use CVS to download code |
| 163 |
updates. More extensive information on using CVS for maintaining |
updates. More extensive information on using CVS for maintaining |
| 164 |
MITgcm code can be found |
MITgcm code can be found |
| 165 |
\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} |
| 166 |
here |
here |
| 167 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 168 |
. |
. |
| 176 |
\end{verbatim} |
\end{verbatim} |
| 177 |
|
|
| 178 |
|
|
| 179 |
\subsubsection{Conventional download method} |
\subsection{Method 2 - Tar file download} |
| 180 |
\label{sect:conventionalDownload} |
\label{sect:conventionalDownload} |
| 181 |
|
|
| 182 |
If you do not have CVS on your system, you can download the model as a |
If you do not have CVS on your system, you can download the model as a |
| 191 |
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 |
| 192 |
tar file does not exist, then please contact the developers through |
tar file does not exist, then please contact the developers through |
| 193 |
the |
the |
| 194 |
\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 195 |
MITgcm-support@mitgcm.org |
MITgcm-support@mitgcm.org |
| 196 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 197 |
mailing list. |
mailing list. |
| 263 |
with. So please be sure you understand what you're doing. |
with. So please be sure you understand what you're doing. |
| 264 |
|
|
| 265 |
\section{Model and directory structure} |
\section{Model and directory structure} |
| 266 |
|
\begin{rawhtml} |
| 267 |
|
<!-- CMIREDIR:directory_structure: --> |
| 268 |
|
\end{rawhtml} |
| 269 |
|
|
| 270 |
The ``numerical'' model is contained within a execution environment |
The ``numerical'' model is contained within a execution environment |
| 271 |
support wrapper. This wrapper is designed to provide a general |
support wrapper. This wrapper is designed to provide a general |
| 273 |
model that uses the framework. Under this structure the model is split |
model that uses the framework. Under this structure the model is split |
| 274 |
into execution environment support code and conventional numerical |
into execution environment support code and conventional numerical |
| 275 |
model code. The execution environment support code is held under the |
model code. The execution environment support code is held under the |
| 276 |
\textit{eesupp} directory. The grid point model code is held under the |
\texttt{eesupp} directory. The grid point model code is held under the |
| 277 |
\textit{model} directory. Code execution actually starts in the |
\texttt{model} directory. Code execution actually starts in the |
| 278 |
\textit{eesupp} routines and not in the \textit{model} routines. For |
\texttt{eesupp} routines and not in the \texttt{model} routines. For |
| 279 |
this reason the top-level \textit{MAIN.F} is in the |
this reason the top-level \texttt{MAIN.F} is in the |
| 280 |
\textit{eesupp/src} directory. In general, end-users should not need |
\texttt{eesupp/src} directory. In general, end-users should not need |
| 281 |
to worry about this level. The top-level routine for the numerical |
to worry about this level. The top-level routine for the numerical |
| 282 |
part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is |
part of the code is in \texttt{model/src/THE\_MODEL\_MAIN.F}. Here is |
| 283 |
a brief description of the directory structure of the model under the |
a brief description of the directory structure of the model under the |
| 284 |
root tree (a detailed description is given in section 3: Code |
root tree (a detailed description is given in section 3: Code |
| 285 |
structure). |
structure). |
| 286 |
|
|
| 287 |
\begin{itemize} |
\begin{itemize} |
| 288 |
|
|
| 289 |
\item \textit{bin}: this directory is initially empty. It is the |
\item \texttt{bin}: this directory is initially empty. It is the |
| 290 |
default directory in which to compile the code. |
default directory in which to compile the code. |
| 291 |
|
|
| 292 |
\item \textit{diags}: contains the code relative to time-averaged |
\item \texttt{diags}: contains the code relative to time-averaged |
| 293 |
diagnostics. It is subdivided into two subdirectories \textit{inc} |
diagnostics. It is subdivided into two subdirectories \texttt{inc} |
| 294 |
and \textit{src} that contain include files (*.\textit{h} files) and |
and \texttt{src} that contain include files (\texttt{*.h} files) and |
| 295 |
Fortran subroutines (*.\textit{F} files), respectively. |
Fortran subroutines (\texttt{*.F} files), respectively. |
| 296 |
|
|
| 297 |
\item \textit{doc}: contains brief documentation notes. |
\item \texttt{doc}: contains brief documentation notes. |
| 298 |
|
|
| 299 |
\item \textit{eesupp}: contains the execution environment source code. |
\item \texttt{eesupp}: contains the execution environment source code. |
| 300 |
Also subdivided into two subdirectories \textit{inc} and |
Also subdivided into two subdirectories \texttt{inc} and |
| 301 |
\textit{src}. |
\texttt{src}. |
| 302 |
|
|
| 303 |
\item \textit{exe}: this directory is initially empty. It is the |
\item \texttt{exe}: this directory is initially empty. It is the |
| 304 |
default directory in which to execute the code. |
default directory in which to execute the code. |
| 305 |
|
|
| 306 |
\item \textit{model}: this directory contains the main source code. |
\item \texttt{model}: this directory contains the main source code. |
| 307 |
Also subdivided into two subdirectories \textit{inc} and |
Also subdivided into two subdirectories \texttt{inc} and |
| 308 |
\textit{src}. |
\texttt{src}. |
| 309 |
|
|
| 310 |
\item \textit{pkg}: contains the source code for the packages. Each |
\item \texttt{pkg}: contains the source code for the packages. Each |
| 311 |
package corresponds to a subdirectory. For example, \textit{gmredi} |
package corresponds to a subdirectory. For example, \texttt{gmredi} |
| 312 |
contains the code related to the Gent-McWilliams/Redi scheme, |
contains the code related to the Gent-McWilliams/Redi scheme, |
| 313 |
\textit{aim} the code relative to the atmospheric intermediate |
\texttt{aim} the code relative to the atmospheric intermediate |
| 314 |
physics. The packages are described in detail in section 3. |
physics. The packages are described in detail in section 3. |
| 315 |
|
|
| 316 |
\item \textit{tools}: this directory contains various useful tools. |
\item \texttt{tools}: this directory contains various useful tools. |
| 317 |
For example, \textit{genmake2} is a script written in csh (C-shell) |
For example, \texttt{genmake2} is a script written in csh (C-shell) |
| 318 |
that should be used to generate your makefile. The directory |
that should be used to generate your makefile. The directory |
| 319 |
\textit{adjoint} contains the makefile specific to the Tangent |
\texttt{adjoint} contains the makefile specific to the Tangent |
| 320 |
linear and Adjoint Compiler (TAMC) that generates the adjoint code. |
linear and Adjoint Compiler (TAMC) that generates the adjoint code. |
| 321 |
The latter is described in details in part V. |
The latter is described in details in part V. |
| 322 |
|
|
| 323 |
\item \textit{utils}: this directory contains various utilities. The |
\item \texttt{utils}: this directory contains various utilities. The |
| 324 |
subdirectory \textit{knudsen2} contains code and a makefile that |
subdirectory \texttt{knudsen2} contains code and a makefile that |
| 325 |
compute coefficients of the polynomial approximation to the knudsen |
compute coefficients of the polynomial approximation to the knudsen |
| 326 |
formula for an ocean nonlinear equation of state. The |
formula for an ocean nonlinear equation of state. The |
| 327 |
\textit{matlab} subdirectory contains matlab scripts for reading |
\texttt{matlab} subdirectory contains matlab scripts for reading |
| 328 |
model output directly into matlab. \textit{scripts} contains C-shell |
model output directly into matlab. \texttt{scripts} contains C-shell |
| 329 |
post-processing scripts for joining processor-based and tiled-based |
post-processing scripts for joining processor-based and tiled-based |
| 330 |
model output. |
model output. |
| 331 |
|
|
| 332 |
\item \textit{verification}: this directory contains the model |
\item \texttt{verification}: this directory contains the model |
| 333 |
examples. See section \ref{sect:modelExamples}. |
examples. See section \ref{sect:modelExamples}. |
| 334 |
|
|
| 335 |
\end{itemize} |
\end{itemize} |
| 336 |
|
|
| 337 |
\section{Example experiments} |
\section[Building MITgcm]{Building the code} |
|
\label{sect:modelExamples} |
|
|
|
|
|
%% a set of twenty-four pre-configured numerical experiments |
|
|
|
|
|
The MITgcm distribution comes with more than a dozen pre-configured |
|
|
numerical experiments. Some of these example experiments are tests of |
|
|
individual parts of the model code, but many are fully fledged |
|
|
numerical simulations. A few of the examples are used for tutorial |
|
|
documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}. |
|
|
The other examples follow the same general structure as the tutorial |
|
|
examples. However, they only include brief instructions in a text file |
|
|
called {\it README}. The examples are located in subdirectories under |
|
|
the directory \textit{verification}. Each example is briefly described |
|
|
below. |
|
|
|
|
|
\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{global\_ocean\_pressure} Global circulation in pressure |
|
|
coordinate (non-Boussinesq ocean model). Described in detail in |
|
|
section \ref{sect:eg-globalpressure}. |
|
|
|
|
|
\item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube |
|
|
sphere grid. |
|
|
|
|
|
\end{enumerate} |
|
|
|
|
|
\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. |
|
|
\end{itemize} |
|
|
|
|
|
In addition, you will also find in this directory the forcing and |
|
|
topography files as well as the files describing the initial state |
|
|
of the experiment. This varies from experiment to experiment. See |
|
|
section 2 for more details. |
|
|
|
|
|
\item \textit{results}: this directory contains the output file |
|
|
\textit{output.txt} produced by the simulation example. This file is |
|
|
useful for comparison with your own output when you run the |
|
|
experiment. |
|
|
\end{itemize} |
|
|
|
|
|
Once you have chosen the example you want to run, you are ready to |
|
|
compile the code. |
|
|
|
|
|
\section{Building the code} |
|
| 338 |
\label{sect:buildingCode} |
\label{sect:buildingCode} |
| 339 |
|
\begin{rawhtml} |
| 340 |
To compile the code, we use the {\em make} program. This uses a file |
<!-- CMIREDIR:buildingCode: --> |
| 341 |
({\em Makefile}) that allows us to pre-process source files, specify |
\end{rawhtml} |
| 342 |
compiler and optimization options and also figures out any file |
|
| 343 |
dependencies. We supply a script ({\em genmake2}), described in |
To compile the code, we use the \texttt{make} program. This uses a |
| 344 |
section \ref{sect:genmake}, that automatically creates the {\em |
file (\texttt{Makefile}) that allows us to pre-process source files, |
| 345 |
Makefile} for you. You then need to build the dependencies and |
specify compiler and optimization options and also figures out any |
| 346 |
|
file dependencies. We supply a script (\texttt{genmake2}), described |
| 347 |
|
in section \ref{sect:genmake}, that automatically creates the |
| 348 |
|
\texttt{Makefile} for you. You then need to build the dependencies and |
| 349 |
compile the code. |
compile the code. |
| 350 |
|
|
| 351 |
As an example, let's assume that you want to build and run experiment |
As an example, assume that you want to build and run experiment |
| 352 |
\textit{verification/exp2}. The are multiple ways and places to |
\texttt{verification/exp2}. The are multiple ways and places to |
| 353 |
actually do this but here let's build the code in |
actually do this but here let's build the code in |
| 354 |
\textit{verification/exp2/input}: |
\texttt{verification/exp2/build}: |
| 355 |
\begin{verbatim} |
\begin{verbatim} |
| 356 |
% cd verification/exp2/input |
% cd verification/exp2/build |
| 357 |
\end{verbatim} |
\end{verbatim} |
| 358 |
First, build the {\em Makefile}: |
First, build the \texttt{Makefile}: |
| 359 |
\begin{verbatim} |
\begin{verbatim} |
| 360 |
% ../../../tools/genmake2 -mods=../code |
% ../../../tools/genmake2 -mods=../code |
| 361 |
\end{verbatim} |
\end{verbatim} |
| 362 |
The command line option tells {\em genmake} to override model source |
The command line option tells \texttt{genmake} to override model source |
| 363 |
code with any files in the directory {\em ./code/}. |
code with any files in the directory \texttt{../code/}. |
| 364 |
|
|
| 365 |
On many systems, the {\em genmake2} program will be able to |
On many systems, the \texttt{genmake2} program will be able to |
| 366 |
automatically recognize the hardware, find compilers and other tools |
automatically recognize the hardware, find compilers and other tools |
| 367 |
within the user's path (``echo \$PATH''), and then choose an |
within the user's path (``\texttt{echo \$PATH}''), and then choose an |
| 368 |
appropriate set of options from the files contained in the {\em |
appropriate set of options from the files (``optfiles'') contained in |
| 369 |
tools/build\_options} directory. Under some circumstances, a user |
the \texttt{tools/build\_options} directory. Under some |
| 370 |
may have to create a new ``optfile'' in order to specify the exact |
circumstances, a user may have to create a new ``optfile'' in order to |
| 371 |
combination of compiler, compiler flags, libraries, and other options |
specify the exact combination of compiler, compiler flags, libraries, |
| 372 |
necessary to build a particular configuration of MITgcm. In such |
and other options necessary to build a particular configuration of |
| 373 |
cases, it is generally helpful to read the existing ``optfiles'' and |
MITgcm. In such cases, it is generally helpful to read the existing |
| 374 |
mimic their syntax. |
``optfiles'' and mimic their syntax. |
| 375 |
|
|
| 376 |
Through the MITgcm-support list, the MITgcm developers are willing to |
Through the MITgcm-support list, the MITgcm developers are willing to |
| 377 |
provide help writing or modifing ``optfiles''. And we encourage users |
provide help writing or modifing ``optfiles''. And we encourage users |
| 378 |
to post new ``optfiles'' (particularly ones for new machines or |
to post new ``optfiles'' (particularly ones for new machines or |
| 379 |
architectures) to the |
architectures) to the |
| 380 |
\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 381 |
MITgcm-support@mitgcm.org |
MITgcm-support@mitgcm.org |
| 382 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 383 |
list. |
list. |
| 384 |
|
|
| 385 |
To specify an optfile to {\em genmake2}, the syntax is: |
To specify an optfile to \texttt{genmake2}, the syntax is: |
| 386 |
\begin{verbatim} |
\begin{verbatim} |
| 387 |
% ../../../tools/genmake2 -mods=../code -of /path/to/optfile |
% ../../../tools/genmake2 -mods=../code -of /path/to/optfile |
| 388 |
\end{verbatim} |
\end{verbatim} |
| 389 |
|
|
| 390 |
Once a {\em Makefile} has been generated, we create the dependencies: |
Once a \texttt{Makefile} has been generated, we create the |
| 391 |
|
dependencies with the command: |
| 392 |
\begin{verbatim} |
\begin{verbatim} |
| 393 |
% make depend |
% make depend |
| 394 |
\end{verbatim} |
\end{verbatim} |
| 395 |
This modifies the {\em Makefile} by attaching a [long] list of files |
This modifies the \texttt{Makefile} by attaching a (usually, long) |
| 396 |
upon which other files depend. The purpose of this is to reduce |
list of files upon which other files depend. The purpose of this is to |
| 397 |
re-compilation if and when you start to modify the code. The {\tt make |
reduce re-compilation if and when you start to modify the code. The |
| 398 |
depend} command also creates links from the model source to this |
{\tt make depend} command also creates links from the model source to |
| 399 |
directory. |
this directory. It is important to note that the {\tt make depend} |
| 400 |
|
stage will occasionally produce warnings or errors since the |
| 401 |
|
dependency parsing tool is unable to find all of the necessary header |
| 402 |
|
files (\textit{eg.} \texttt{netcdf.inc}). In these circumstances, it |
| 403 |
|
is usually OK to ignore the warnings/errors and proceed to the next |
| 404 |
|
step. |
| 405 |
|
|
| 406 |
Next compile the code: |
Next one can compile the code using: |
| 407 |
\begin{verbatim} |
\begin{verbatim} |
| 408 |
% make |
% make |
| 409 |
\end{verbatim} |
\end{verbatim} |
| 410 |
The {\tt make} command creates an executable called \textit{mitgcmuv}. |
The {\tt make} command creates an executable called \texttt{mitgcmuv}. |
| 411 |
Additional make ``targets'' are defined within the makefile to aid in |
Additional make ``targets'' are defined within the makefile to aid in |
| 412 |
the production of adjoint and other versions of MITgcm. |
the production of adjoint and other versions of MITgcm. On SMP |
| 413 |
|
(shared multi-processor) systems, the build process can often be sped |
| 414 |
|
up appreciably using the command: |
| 415 |
|
\begin{verbatim} |
| 416 |
|
% make -j 2 |
| 417 |
|
\end{verbatim} |
| 418 |
|
where the ``2'' can be replaced with a number that corresponds to the |
| 419 |
|
number of CPUs available. |
| 420 |
|
|
| 421 |
Now you are ready to run the model. General instructions for doing so are |
Now you are ready to run the model. General instructions for doing so are |
| 422 |
given in section \ref{sect:runModel}. Here, we can run the model with: |
given in section \ref{sect:runModel}. Here, we can run the model by |
| 423 |
|
first creating links to all the input files: |
| 424 |
|
\begin{verbatim} |
| 425 |
|
ln -s ../input/* . |
| 426 |
|
\end{verbatim} |
| 427 |
|
and then calling the executable with: |
| 428 |
\begin{verbatim} |
\begin{verbatim} |
| 429 |
./mitgcmuv > output.txt |
./mitgcmuv > output.txt |
| 430 |
\end{verbatim} |
\end{verbatim} |
| 431 |
where we are re-directing the stream of text output to the file {\em |
where we are re-directing the stream of text output to the file |
| 432 |
output.txt}. |
\texttt{output.txt}. |
|
|
|
| 433 |
|
|
| 434 |
\subsection{Building/compiling the code elsewhere} |
\subsection{Building/compiling the code elsewhere} |
| 435 |
|
|
| 802 |
|
|
| 803 |
\end{enumerate} |
\end{enumerate} |
| 804 |
|
|
| 805 |
|
An example of the above process on the MITgcm cluster (``cg01'') using |
| 806 |
|
the GNU g77 compiler and the mpich MPI library is: |
| 807 |
|
|
| 808 |
|
{\footnotesize \begin{verbatim} |
| 809 |
|
% cd MITgcm/verification/exp5 |
| 810 |
|
% mkdir build |
| 811 |
|
% cd build |
| 812 |
|
% ../../../tools/genmake2 -mpi -mods=../code \ |
| 813 |
|
-of=../../../tools/build_options/linux_ia32_g77+mpi_cg01 |
| 814 |
|
% make depend |
| 815 |
|
% make |
| 816 |
|
% cd ../input |
| 817 |
|
% /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \ |
| 818 |
|
-machinefile mf --gm-kill 5 -v -np 2 ../build/mitgcmuv |
| 819 |
|
\end{verbatim} } |
| 820 |
|
|
| 821 |
\section{Running the model} |
\section[Running MITgcm]{Running the model in prognostic mode} |
| 822 |
\label{sect:runModel} |
\label{sect:runModel} |
| 823 |
|
\begin{rawhtml} |
| 824 |
|
<!-- CMIREDIR:runModel: --> |
| 825 |
|
\end{rawhtml} |
| 826 |
|
|
| 827 |
If compilation finished succesfuully (section \ref{sect:buildingCode}) |
If compilation finished succesfully (section \ref{sect:buildingCode}) |
| 828 |
then an executable called \texttt{mitgcmuv} will now exist in the |
then an executable called \texttt{mitgcmuv} will now exist in the |
| 829 |
local directory. |
local directory. |
| 830 |
|
|
| 831 |
To run the model as a single process (ie. not in parallel) simply |
To run the model as a single process (\textit{ie.} not in parallel) |
| 832 |
type: |
simply type: |
| 833 |
\begin{verbatim} |
\begin{verbatim} |
| 834 |
% ./mitgcmuv |
% ./mitgcmuv |
| 835 |
\end{verbatim} |
\end{verbatim} |
| 839 |
your screen. This output contains details such as parameter values as |
your screen. This output contains details such as parameter values as |
| 840 |
well as diagnostics such as mean Kinetic energy, largest CFL number, |
well as diagnostics such as mean Kinetic energy, largest CFL number, |
| 841 |
etc. It is worth keeping this text output with the binary output so we |
etc. It is worth keeping this text output with the binary output so we |
| 842 |
normally re-direct the {\em stdout} stream as follows: |
normally re-direct the \texttt{stdout} stream as follows: |
| 843 |
\begin{verbatim} |
\begin{verbatim} |
| 844 |
% ./mitgcmuv > output.txt |
% ./mitgcmuv > output.txt |
| 845 |
\end{verbatim} |
\end{verbatim} |
| 846 |
|
In the event that the model encounters an error and stops, it is very |
| 847 |
For the example experiments in {\em verification}, an example of the |
helpful to include the last few line of this \texttt{output.txt} file |
| 848 |
output is kept in {\em results/output.txt} for comparison. You can compare |
along with the (\texttt{stderr}) error message within any bug reports. |
| 849 |
your {\em output.txt} with this one to check that the set-up works. |
|
| 850 |
|
For the example experiments in \texttt{verification}, an example of the |
| 851 |
|
output is kept in \texttt{results/output.txt} for comparison. You can |
| 852 |
|
compare your \texttt{output.txt} with the corresponding one for that |
| 853 |
|
experiment to check that the set-up works. |
| 854 |
|
|
| 855 |
|
|
| 856 |
|
|
| 857 |
\subsection{Output files} |
\subsection{Output files} |
| 858 |
|
|
| 859 |
The model produces various output files. At a minimum, the instantaneous |
The model produces various output files and, when using \texttt{mnc}, |
| 860 |
``state'' of the model is written out, which is made of the following files: |
sometimes even directories. Depending upon the I/O package(s) |
| 861 |
|
selected at compile time (either \texttt{mdsio} or \texttt{mnc} or |
| 862 |
|
both as determined by \texttt{code/packages.conf}) and the run-time |
| 863 |
|
flags set (in \texttt{input/data.pkg}), the following output may |
| 864 |
|
appear. |
| 865 |
|
|
| 866 |
|
|
| 867 |
|
\subsubsection{MDSIO output files} |
| 868 |
|
|
| 869 |
|
The ``traditional'' output files are generated by the \texttt{mdsio} |
| 870 |
|
package. At a minimum, the instantaneous ``state'' of the model is |
| 871 |
|
written out, which is made of the following files: |
| 872 |
|
|
| 873 |
\begin{itemize} |
\begin{itemize} |
| 874 |
\item \textit{U.00000nIter} - zonal component of velocity field (m/s and $> |
\item \texttt{U.00000nIter} - zonal component of velocity field (m/s |
| 875 |
0 $ eastward). |
and positive eastward). |
| 876 |
|
|
| 877 |
\item \textit{V.00000nIter} - meridional component of velocity field (m/s |
\item \texttt{V.00000nIter} - meridional component of velocity field |
| 878 |
and $> 0$ northward). |
(m/s and positive northward). |
| 879 |
|
|
| 880 |
\item \textit{W.00000nIter} - vertical component of velocity field (ocean: |
\item \texttt{W.00000nIter} - vertical component of velocity field |
| 881 |
m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure |
(ocean: m/s and positive upward, atmosphere: Pa/s and positive |
| 882 |
i.e. downward). |
towards increasing pressure i.e. downward). |
| 883 |
|
|
| 884 |
\item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C, |
\item \texttt{T.00000nIter} - potential temperature (ocean: |
| 885 |
atmosphere: $^{0}$K). |
$^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$). |
| 886 |
|
|
| 887 |
\item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor |
\item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water |
| 888 |
(g/kg). |
vapor (g/kg). |
| 889 |
|
|
| 890 |
\item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere: |
\item \texttt{Eta.00000nIter} - ocean: surface elevation (m), |
| 891 |
surface pressure anomaly (Pa). |
atmosphere: surface pressure anomaly (Pa). |
| 892 |
\end{itemize} |
\end{itemize} |
| 893 |
|
|
| 894 |
The chain \textit{00000nIter} consists of ten figures that specify the |
The chain \texttt{00000nIter} consists of ten figures that specify the |
| 895 |
iteration number at which the output is written out. For example, \textit{% |
iteration number at which the output is written out. For example, |
| 896 |
U.0000000300} is the zonal velocity at iteration 300. |
\texttt{U.0000000300} is the zonal velocity at iteration 300. |
| 897 |
|
|
| 898 |
In addition, a ``pickup'' or ``checkpoint'' file called: |
In addition, a ``pickup'' or ``checkpoint'' file called: |
| 899 |
|
|
| 900 |
\begin{itemize} |
\begin{itemize} |
| 901 |
\item \textit{pickup.00000nIter} |
\item \texttt{pickup.00000nIter} |
| 902 |
\end{itemize} |
\end{itemize} |
| 903 |
|
|
| 904 |
is written out. This file represents the state of the model in a condensed |
is written out. This file represents the state of the model in a condensed |
| 906 |
there is an additional ``pickup'' file: |
there is an additional ``pickup'' file: |
| 907 |
|
|
| 908 |
\begin{itemize} |
\begin{itemize} |
| 909 |
\item \textit{pickup\_cd.00000nIter} |
\item \texttt{pickup\_cd.00000nIter} |
| 910 |
\end{itemize} |
\end{itemize} |
| 911 |
|
|
| 912 |
containing the D-grid velocity data and that has to be written out as well |
containing the D-grid velocity data and that has to be written out as well |
| 913 |
in order to restart the integration. Rolling checkpoint files are the same |
in order to restart the integration. Rolling checkpoint files are the same |
| 914 |
as the pickup files but are named differently. Their name contain the chain |
as the pickup files but are named differently. Their name contain the chain |
| 915 |
\textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be |
\texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be |
| 916 |
used to restart the model but are overwritten every other time they are |
used to restart the model but are overwritten every other time they are |
| 917 |
output to save disk space during long integrations. |
output to save disk space during long integrations. |
| 918 |
|
|
| 919 |
|
|
| 920 |
|
|
| 921 |
|
\subsubsection{MNC output files} |
| 922 |
|
|
| 923 |
|
Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output |
| 924 |
|
is usually (though not necessarily) placed within a subdirectory with |
| 925 |
|
a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}. The files |
| 926 |
|
within this subdirectory are all in the ``self-describing'' netCDF |
| 927 |
|
format and can thus be browsed and/or plotted using tools such as: |
| 928 |
|
\begin{itemize} |
| 929 |
|
\item \texttt{ncdump} is a utility which is typically included |
| 930 |
|
with every netCDF install: |
| 931 |
|
\begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml} |
| 932 |
|
\begin{verbatim} |
| 933 |
|
http://www.unidata.ucar.edu/packages/netcdf/ |
| 934 |
|
\end{verbatim} |
| 935 |
|
\begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF |
| 936 |
|
binaries into formatted ASCII text files. |
| 937 |
|
|
| 938 |
|
\item \texttt{ncview} utility is a very convenient and quick way |
| 939 |
|
to plot netCDF data and it runs on most OSes: |
| 940 |
|
\begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml} |
| 941 |
|
\begin{verbatim} |
| 942 |
|
http://meteora.ucsd.edu/~pierce/ncview_home_page.html |
| 943 |
|
\end{verbatim} |
| 944 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 945 |
|
|
| 946 |
|
\item MatLAB(c) and other common post-processing environments provide |
| 947 |
|
various netCDF interfaces including: |
| 948 |
|
\begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml} |
| 949 |
|
\begin{verbatim} |
| 950 |
|
http://mexcdf.sourceforge.net/ |
| 951 |
|
\end{verbatim} |
| 952 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 953 |
|
\begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml} |
| 954 |
|
\begin{verbatim} |
| 955 |
|
http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html |
| 956 |
|
\end{verbatim} |
| 957 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 958 |
|
\end{itemize} |
| 959 |
|
|
| 960 |
|
|
| 961 |
\subsection{Looking at the output} |
\subsection{Looking at the output} |
| 962 |
|
|
| 963 |
All the model data are written according to a ``meta/data'' file format. |
The ``traditional'' or mdsio model data are written according to a |
| 964 |
Each variable is associated with two files with suffix names \textit{.data} |
``meta/data'' file format. Each variable is associated with two files |
| 965 |
and \textit{.meta}. The \textit{.data} file contains the data written in |
with suffix names \texttt{.data} and \texttt{.meta}. The |
| 966 |
binary form (big\_endian by default). The \textit{.meta} file is a |
\texttt{.data} file contains the data written in binary form |
| 967 |
``header'' file that contains information about the size and the structure |
(big\_endian by default). The \texttt{.meta} file is a ``header'' file |
| 968 |
of the \textit{.data} file. This way of organizing the output is |
that contains information about the size and the structure of the |
| 969 |
particularly useful when running multi-processors calculations. The base |
\texttt{.data} file. This way of organizing the output is particularly |
| 970 |
version of the model includes a few matlab utilities to read output files |
useful when running multi-processors calculations. The base version of |
| 971 |
written in this format. The matlab scripts are located in the directory |
the model includes a few matlab utilities to read output files written |
| 972 |
\textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads |
in this format. The matlab scripts are located in the directory |
| 973 |
the data. Look at the comments inside the script to see how to use it. |
\texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m} |
| 974 |
|
reads the data. Look at the comments inside the script to see how to |
| 975 |
|
use it. |
| 976 |
|
|
| 977 |
Some examples of reading and visualizing some output in {\em Matlab}: |
Some examples of reading and visualizing some output in {\em Matlab}: |
| 978 |
\begin{verbatim} |
\begin{verbatim} |
| 989 |
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end |
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end |
| 990 |
\end{verbatim} |
\end{verbatim} |
| 991 |
|
|
| 992 |
\section{Doing it yourself: customizing the code} |
Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and |
| 993 |
|
they are described in Section \ref{sec:pkg:mnc}. |
|
When you are ready to run the model in the configuration you want, the |
|
|
easiest thing is to use and adapt the setup of the case studies |
|
|
experiment (described previously) that is the closest to your |
|
|
configuration. Then, the amount of setup will be minimized. In this |
|
|
section, we focus on the setup relative to the ``numerical model'' |
|
|
part of the code (the setup relative to the ``execution environment'' |
|
|
part is covered in the parallel implementation section) and on the |
|
|
variables and parameters that you are likely to change. |
|
|
|
|
|
\subsection{Configuration and setup} |
|
|
|
|
|
The CPP keys relative to the ``numerical model'' part of the code are |
|
|
all defined and set in the file \textit{CPP\_OPTIONS.h }in the |
|
|
directory \textit{ model/inc }or in one of the \textit{code |
|
|
}directories of the case study experiments under |
|
|
\textit{verification.} The model parameters are defined and declared |
|
|
in the file \textit{model/inc/PARAMS.h }and their default values are |
|
|
set in the routine \textit{model/src/set\_defaults.F. }The default |
|
|
values can be modified in the namelist file \textit{data }which needs |
|
|
to be located in the directory where you will run the model. The |
|
|
parameters are initialized in the routine |
|
|
\textit{model/src/ini\_parms.F}. Look at this routine to see in what |
|
|
part of the namelist the parameters are located. |
|
|
|
|
|
In what follows the parameters are grouped into categories related to |
|
|
the computational domain, the equations solved in the model, and the |
|
|
simulation controls. |
|
|
|
|
|
\subsection{Computational domain, geometry and time-discretization} |
|
|
|
|
|
\begin{description} |
|
|
\item[dimensions] \ |
|
|
|
|
|
The number of points in the x, y, and r directions are represented |
|
|
by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr} |
|
|
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 the section on |
|
|
parallel implementation.) |
|
|
|
|
|
\item[grid] \ |
|
|
|
|
|
Three different grids are available: cartesian, spherical polar, and |
|
|
curvilinear (which includes the cubed sphere). The grid is set |
|
|
through the logical variables \textbf{usingCartesianGrid}, |
|
|
\textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}. |
|
|
In the case of spherical and curvilinear grids, the southern |
|
|
boundary is defined through the variable \textbf{phiMin} 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} and \textbf{dely} (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} 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 puts 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} and \textbf{beta} 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 } is set to a nonzero value, \textbf{f0} is the |
|
|
value of $f$ at the southern edge of the domain. |
|
|
|
|
|
\item[topography - full and partial cells] \ |
|
|
|
|
|
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}. 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} |
|
|
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} 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} or \textbf{delp}. |
|
|
The model will interpolate the numbers in \textbf{bathyFile} so that |
|
|
they match the levels obtained from \textbf{delz} or \textbf{delp} |
|
|
and \textbf{hFacMin}. |
|
|
|
|
|
(Note: the atmospheric case is a bit more complicated than what is |
|
|
written here I think. To come soon...) |
|
|
|
|
|
\item[time-discretization] \ |
|
|
|
|
|
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.'}. |
|
|
|
|
|
\end{description} |
|
|
|
|
|
|
|
|
\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} to |
|
|
\texttt{'POLYNOMIAL'}). In the linear case, you need to specify the |
|
|
thermal and haline expansion coefficients represented by the variables |
|
|
\textbf{tAlpha} (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; {\em 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} and \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{description} |
|
|
\item[initialization] \ |
|
|
|
|
|
The velocity components are initialized to 0 unless the simulation |
|
|
is starting from a pickup file (see section on simulation control |
|
|
parameters). |
|
|
|
|
|
\item[forcing] \ |
|
|
|
|
|
This section only applies to the ocean. You need to generate |
|
|
wind-stress data into two files \textbf{zonalWindFile} 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}. 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. |
|
|
|
|
|
\item[dissipation] \ |
|
|
|
|
|
The lateral eddy viscosity coefficient is specified through the |
|
|
variable \textbf{viscAh} (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} (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} (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} 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} in s$ ^{-1}$) and |
|
|
quadratic (set the variable \textbf{bottomDragQuadratic} in |
|
|
m$^{-1}$). |
|
|
|
|
|
The Fourier and Shapiro filters are described elsewhere. |
|
|
|
|
|
\item[C-D scheme] \ |
|
|
|
|
|
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. |
|
|
|
|
|
\item[calculation of pressure/geopotential] \ |
|
|
|
|
|
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} and \textbf{cg2dTargetResidual } for |
|
|
the 2D case and \textbf{cg3dMaxIters} 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} |
|
|
(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). |
|
|
|
|
|
\end{description} |
|
|
|
|
|
\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} \textbf{tempAdvection} |
|
|
\textbf{tempForcing}, 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}, |
|
|
\textbf{saltAdvection} 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{description} |
|
|
\item[initialization] \ |
|
|
|
|
|
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. |
|
|
|
|
|
\item[forcing] \ |
|
|
|
|
|
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}$) can be stored in the 2D binary file |
|
|
\textbf{surfQfile}. Alternatively or in addition, the forcing can |
|
|
be specified through a relaxation term. The SST data to which the |
|
|
model surface temperatures are restored to are supposed to be stored |
|
|
in the 2D binary file \textbf{thetaClimFile}. The corresponding |
|
|
relaxation time scale coefficient is set through the variable |
|
|
\textbf{tauThetaClimRelax} (in s). The same procedure applies for |
|
|
salinity with the variable names \textbf{EmPmRfile}, |
|
|
\textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater |
|
|
flux (in m/s) and surface salinity (in ppt) data files and |
|
|
relaxation time scale coefficient (in s), respectively. Also for |
|
|
salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, |
|
|
natural boundary conditions are applied i.e. when computing the |
|
|
surface salinity tendency, the freshwater flux is multiplied by the |
|
|
model surface salinity instead of a constant salinity value. |
|
|
|
|
|
As for the other input files, the precision with which to read the |
|
|
data is controlled by the variable \textbf{readBinaryPrec}. |
|
|
Time-dependent, periodic forcing can be applied as well following |
|
|
the same procedure used for the wind forcing data (see above). |
|
|
|
|
|
\item[dissipation] \ |
|
|
|
|
|
Lateral eddy diffusivities for temperature and salinity/specific |
|
|
humidity are specified through the variables \textbf{diffKhT} and |
|
|
\textbf{diffKhS} (in m$^{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}$/s). Note that the cosine power scaling (specified through |
|
|
\textbf{cosPower}---see the momentum equations section) is applied to |
|
|
the tracer diffusivities (Laplacian and biharmonic) as well. The |
|
|
Gent and McWilliams parameterization for oceanic tracers is |
|
|
described in the package section. Finally, note that tracers can be |
|
|
also subject to Fourier and Shapiro filtering (see the corresponding |
|
|
section on these filters). |
|
|
|
|
|
\item[ocean convection] \ |
|
|
|
|
|
Two options are available to parameterize ocean convection: one is |
|
|
to use the convective adjustment scheme. In this case, you need to |
|
|
set the variable \textbf{cadjFreq}, which represents the frequency |
|
|
(in s) with which the adjustment algorithm is called, to a non-zero |
|
|
value (if set to a negative value by the user, the model will set it |
|
|
to the tracer time step). The other option is to parameterize |
|
|
convection with implicit vertical diffusion. To do this, set the |
|
|
logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'} |
|
|
and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s) |
|
|
you wish the tracer vertical diffusivities to have when mixing |
|
|
tracers vertically due to static instabilities. Note that |
|
|
\textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero |
|
|
value. |
|
|
|
|
|
\end{description} |
|
|
|
|
|
\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{description} |
|
|
\item[run duration] \ |
|
|
|
|
|
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. 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}. |
|
|
|
|
|
\item[frequency of output] \ |
|
|
|
|
|
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}). |
|
|
|
|
|
\end{description} |
|
|
|
|
| 994 |
|
|
|
%%% Local Variables: |
|
|
%%% mode: latex |
|
|
%%% TeX-master: t |
|
|
%%% End: |
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