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revision 1.17 by edhill, Thu Jan 29 15:11:39 2004 UTC revision 1.38 by molod, Wed Jun 28 17:20:51 2006 UTC
# Line 17  you are ready to try implementing the co Line 17  you are ready to try implementing the co
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:  There is a web-archived support mailing list for the model that
 \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/pelican  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 Here you will find an on-line version of this document, a  
 ``browsable'' copy of the code and a searchable database of the model  
 and site, as well as links for downloading the model and  
 documentation, to data-sources, and other related sites.  
   
 There is also a web-archived support mailing list for the model that  
25  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
26  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
27  \begin{verbatim}  \begin{verbatim}
# Line 37  http://mitgcm.org/mailman/listinfo/mitgc Line 29  http://mitgcm.org/mailman/listinfo/mitgc
29  http://mitgcm.org/pipermail/mitgcm-support/  http://mitgcm.org/pipermail/mitgcm-support/
30  \end{verbatim}  \end{verbatim}
31  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
 Essentially all of the MITgcm web pages can be searched using a  
 popular web crawler such as Google or through our own search facility:  
 \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/htdig/  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org  
   
   
32    
33  \section{Obtaining the code}  \section{Obtaining the code}
34  \label{sect:obtainingCode}  \label{sect:obtainingCode}
35    \begin{rawhtml}
36    <!-- CMIREDIR:obtainingCode: -->
37    \end{rawhtml}
38    
39  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
40  the instructions below. As a courtesy we ask that you send e-mail to us at  the instructions below. As a courtesy we ask that you send e-mail to us at
# Line 79  provide easy support for maintenance upd Line 64  provide easy support for maintenance upd
64    
65  \end{enumerate}  \end{enumerate}
66    
67    \subsection{Method 1 - Checkout from CVS}
68    \label{sect:cvs_checkout}
69    
70  If CVS is available on your system, we strongly encourage you to use it. CVS  If CVS is available on your system, we strongly encourage you to use it. CVS
71  provides an efficient and elegant way of organizing your code and keeping  provides an efficient and elegant way of organizing your code and keeping
72  track of your changes. If CVS is not available on your machine, you can also  track of your changes. If CVS is not available on your machine, you can also
# Line 89  be set within your shell.  For a csh or Line 77  be set within your shell.  For a csh or
77  \begin{verbatim}  \begin{verbatim}
78  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
79  \end{verbatim}  \end{verbatim}
80  in your .cshrc or .tcshrc file.  For bash or sh shells, put:  in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
81    shells, put:
82  \begin{verbatim}  \begin{verbatim}
83  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
84  \end{verbatim}  \end{verbatim}
85  in your .profile or .bashrc file.  in your \texttt{.profile} or \texttt{.bashrc} file.
86    
87    
88  To get MITgcm through CVS, first register with the MITgcm CVS server  To get MITgcm through CVS, first register with the MITgcm CVS server
# Line 115  The MITgcm web site contains further dir Line 104  The MITgcm web site contains further dir
104  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
105  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
106  development milestones:  development milestones:
107  \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
108  \begin{verbatim}  \begin{verbatim}
109  http://mitgcm.org/source_code.html  http://mitgcm.org/source_code.html
110  \end{verbatim}  \end{verbatim}
111  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
112    
113    As a convenience, the MITgcm CVS server contains aliases which are
114    named subsets of the codebase.  These aliases can be especially
115    helpful when used over slow internet connections or on machines with
116    restricted storage space.  Table \ref{tab:cvsModules} contains a list
117    of CVS aliases
118    \begin{table}[htb]
119      \centering
120      \begin{tabular}[htb]{|lp{3.25in}|}\hline
121        \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline
122        \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\
123        \texttt{MITgcm\_verif\_basic}
124        &  Source code plus a small set of the verification examples
125        (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5},
126        \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\
127        \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\
128        \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\
129        \texttt{MITgcm\_verif\_all}    &  Source code plus all of the
130        verification examples. \\\hline
131      \end{tabular}
132      \caption{MITgcm CVS Modules}
133      \label{tab:cvsModules}
134    \end{table}
135    
136  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \texttt{MITgcm}. If
137  the directory \textit{MITgcm} exists this command updates your code  the directory \texttt{MITgcm} exists this command updates your code
138  based on the repository. Each directory in the source tree contains a  based on the repository. Each directory in the source tree contains a
139  directory \textit{CVS}. This information is required by CVS to keep  directory \texttt{CVS}. This information is required by CVS to keep
140  track of your file versions with respect to the repository. Don't edit  track of your file versions with respect to the repository. Don't edit
141  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
142  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
143  MITgcm code can be found  MITgcm code can be found
144  \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}
145  here  here
146  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
147  .  .
148    It is important to note that the CVS aliases in Table
149    \ref{tab:cvsModules} cannot be used in conjunction with the CVS
150  \paragraph*{Conventional download method}  \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
151  \label{sect:conventionalDownload}  they create can be changed to a different name following the check-out:
   
 If you do not have CVS on your system, you can download the model as a  
 tar file from the web site at:  
 \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  
152  \begin{verbatim}  \begin{verbatim}
153  http://mitgcm.org/download/     %  cvs co MITgcm_verif_basic
154       %  mv MITgcm MITgcm_verif_basic
155  \end{verbatim}  \end{verbatim}
 \begin{rawhtml} </A> \end{rawhtml}  
 The tar file still contains CVS information which we urge you not to  
 delete; even if you do not use CVS yourself the information can help  
 us if you should need to send us your copy of the code.  If a recent  
 tar file does not exist, then please contact the developers through  
 the  
 \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  
 MITgcm-support@mitgcm.org  
 \begin{rawhtml} </A> \end{rawhtml}  
 mailing list.  
156    
157  \paragraph*{Upgrading from an earlier version}  \subsubsection{Upgrading from an earlier version}
158    
159  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''
160  your copy instead of downloading the entire repository again. First,  your copy instead of downloading the entire repository again. First,
# Line 222  that you may only have part of a patch. Line 220  that you may only have part of a patch.
220  also means we can't tell what version of the code you are working  also means we can't tell what version of the code you are working
221  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
222    
223    \subsection{Method 2 - Tar file download}
224    \label{sect:conventionalDownload}
225    
226    If you do not have CVS on your system, you can download the model as a
227    tar file from the web site at:
228    \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
229    \begin{verbatim}
230    http://mitgcm.org/download/
231    \end{verbatim}
232    \begin{rawhtml} </A> \end{rawhtml}
233    The tar file still contains CVS information which we urge you not to
234    delete; even if you do not use CVS yourself the information can help
235    us if you should need to send us your copy of the code.  If a recent
236    tar file does not exist, then please contact the developers through
237    the
238    \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
239    MITgcm-support@mitgcm.org
240    \begin{rawhtml} </A> \end{rawhtml}
241    mailing list.
242    
243  \section{Model and directory structure}  \section{Model and directory structure}
244    \begin{rawhtml}
245    <!-- CMIREDIR:directory_structure: -->
246    \end{rawhtml}
247    
248  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
249  support wrapper. This wrapper is designed to provide a general  support wrapper. This wrapper is designed to provide a general
# Line 230  framework for grid-point models. MITgcmU Line 251  framework for grid-point models. MITgcmU
251  model that uses the framework. Under this structure the model is split  model that uses the framework. Under this structure the model is split
252  into execution environment support code and conventional numerical  into execution environment support code and conventional numerical
253  model code. The execution environment support code is held under the  model code. The execution environment support code is held under the
254  \textit{eesupp} directory. The grid point model code is held under the  \texttt{eesupp} directory. The grid point model code is held under the
255  \textit{model} directory. Code execution actually starts in the  \texttt{model} directory. Code execution actually starts in the
256  \textit{eesupp} routines and not in the \textit{model} routines. For  \texttt{eesupp} routines and not in the \texttt{model} routines. For
257  this reason the top-level \textit{MAIN.F} is in the  this reason the top-level \texttt{MAIN.F} is in the
258  \textit{eesupp/src} directory. In general, end-users should not need  \texttt{eesupp/src} directory. In general, end-users should not need
259  to worry about this level. The top-level routine for the numerical  to worry about this level. The top-level routine for the numerical
260  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
261  a brief description of the directory structure of the model under the  a brief description of the directory structure of the model under the
262  root tree (a detailed description is given in section 3: Code  root tree (a detailed description is given in section 3: Code
263  structure).  structure).
264    
265  \begin{itemize}  \begin{itemize}
266    
267  \item \textit{bin}: this directory is initially empty. It is the  \item \texttt{doc}: contains brief documentation notes.
   default directory in which to compile the code.  
     
 \item \textit{diags}: contains the code relative to time-averaged  
   diagnostics. It is subdivided into two subdirectories \textit{inc}  
   and \textit{src} that contain include files (*.\textit{h} files) and  
   Fortran subroutines (*.\textit{F} files), respectively.  
   
 \item \textit{doc}: contains brief documentation notes.  
     
 \item \textit{eesupp}: contains the execution environment source code.  
   Also subdivided into two subdirectories \textit{inc} and  
   \textit{src}.  
268        
269  \item \textit{exe}: this directory is initially empty. It is the  \item \texttt{eesupp}: contains the execution environment source code.
270    default directory in which to execute the code.    Also subdivided into two subdirectories \texttt{inc} and
271      \texttt{src}.
272      
273    \item \texttt{model}: this directory contains the main source code.
274      Also subdivided into two subdirectories \texttt{inc} and
275      \texttt{src}.
276        
277  \item \textit{model}: this directory contains the main source code.  \item \texttt{pkg}: contains the source code for the packages. Each
278    Also subdivided into two subdirectories \textit{inc} and    package corresponds to a subdirectory. For example, \texttt{gmredi}
   \textit{src}.  
     
 \item \textit{pkg}: contains the source code for the packages. Each  
   package corresponds to a subdirectory. For example, \textit{gmredi}  
279    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
280    \textit{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
281    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in chapter \ref{chap.packagesI}.
282        
283  \item \textit{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
284    For example, \textit{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
285    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
286    \textit{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
287    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
288    The latter is described in details in part V.    The latter is described in detail in part \ref{chap.ecco}.
289      This directory also contains the subdirectory build\_options, which
290      contains the `optfiles' with the compiler options for the different
291      compilers and machines that can run MITgcm.
292        
293  \item \textit{utils}: this directory contains various utilities. The  \item \texttt{utils}: this directory contains various utilities. The
294    subdirectory \textit{knudsen2} contains code and a makefile that    subdirectory \texttt{knudsen2} contains code and a makefile that
295    compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
296    formula for an ocean nonlinear equation of state. The    formula for an ocean nonlinear equation of state. The
297    \textit{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
298    model output directly into matlab. \textit{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
299    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
300    model output.    model output. The subdirectory exch2 contains the code needed for
301      the exch2 package to work with different combinations of domain
302      decompositions.
303        
304  \item \textit{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
305    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sect:modelExamples}.
306    
307  \end{itemize}  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
   
 \section{Example experiments}  
 \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.  
308        
309  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  \item \texttt{lsopt}: Line search code used for optimization.
   scheme; 1 month integration  
310        
311  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and  \item \texttt{optim}: Interface between MITgcm and line search code.
   Suarez '94 forcing.  
312        
 \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.  
313  \end{itemize}  \end{itemize}
314    
315  Once you have chosen the example you want to run, you are ready to  \section[Building MITgcm]{Building the code}
 compile the code.  
   
 \section{Building the code}  
316  \label{sect:buildingCode}  \label{sect:buildingCode}
317    \begin{rawhtml}
318  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
319  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
320  compiler and optimization options and also figures out any file  
321  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
322  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
323    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
324    file dependencies. We supply a script (\texttt{genmake2}), described
325    in section \ref{sect:genmake}, that automatically creates the
326    \texttt{Makefile} for you. You then need to build the dependencies and
327  compile the code.  compile the code.
328    
329  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
330  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
331  actually do this but here let's build the code in  actually do this but here let's build the code in
332  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
333  \begin{verbatim}  \begin{verbatim}
334  % cd verification/exp2/input  % cd verification/exp2/build
335  \end{verbatim}  \end{verbatim}
336  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
337  \begin{verbatim}  \begin{verbatim}
338  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
339  \end{verbatim}  \end{verbatim}
340  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
341  code with any files in the directory {\em ./code/}.  code with any files in the directory \texttt{../code/}.
342    
343  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
344  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
345  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
346  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
347    tools/build\_options} directory.  Under some circumstances, a user  the \texttt{tools/build\_options} directory.  Under some
348  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
349  combination of compiler, compiler flags, libraries, and other options  specify the exact combination of compiler, compiler flags, libraries,
350  necessary to build a particular configuration of MITgcm.  In such  and other options necessary to build a particular configuration of
351  cases, it is generally helpful to read the existing ``optfiles'' and  MITgcm.  In such cases, it is generally helpful to read the existing
352  mimic their syntax.  ``optfiles'' and mimic their syntax.
353    
354  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
355  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
356  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
357  architectures) to the  architectures) to the
358  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
359  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
360  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
361  list.  list.
362    
363  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
364  \begin{verbatim}  \begin{verbatim}
365  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
366  \end{verbatim}  \end{verbatim}
367    
368  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
369    dependencies with the command:
370  \begin{verbatim}  \begin{verbatim}
371  % make depend  % make depend
372  \end{verbatim}  \end{verbatim}
373  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
374  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
375  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
376    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
377  directory.  this directory.  It is important to note that the {\tt make depend}
378    stage will occasionally produce warnings or errors since the
379    dependency parsing tool is unable to find all of the necessary header
380    files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
381    is usually OK to ignore the warnings/errors and proceed to the next
382    step.
383    
384  Next compile the code:  Next one can compile the code using:
385  \begin{verbatim}  \begin{verbatim}
386  % make  % make
387  \end{verbatim}  \end{verbatim}
388  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
389  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
390  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
391    (shared multi-processor) systems, the build process can often be sped
392    up appreciably using the command:
393    \begin{verbatim}
394    % make -j 2
395    \end{verbatim}
396    where the ``2'' can be replaced with a number that corresponds to the
397    number of CPUs available.
398    
399  Now you are ready to run the model. General instructions for doing so are  Now you are ready to run the model. General instructions for doing so are
400  given in section \ref{sect:runModel}. Here, we can run the model with:  given in section \ref{sect:runModel}. Here, we can run the model by
401    first creating links to all the input files:
402    \begin{verbatim}
403    ln -s ../input/* .
404    \end{verbatim}
405    and then calling the executable with:
406  \begin{verbatim}  \begin{verbatim}
407  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
408  \end{verbatim}  \end{verbatim}
409  where we are re-directing the stream of text output to the file {\em  where we are re-directing the stream of text output to the file
410  output.txt}.  \texttt{output.txt}.
   
411    
412  \subsection{Building/compiling the code elsewhere}  \subsection{Building/compiling the code elsewhere}
413    
# Line 633  the one experiment: Line 514  the one experiment:
514  \end{verbatim}  \end{verbatim}
515    
516    
517    \subsection{Using \texttt{genmake2}}
 \subsection{Using \textit{genmake2}}  
518  \label{sect:genmake}  \label{sect:genmake}
519    
520  To compile the code, first use the program \texttt{genmake2} (located  To compile the code, first use the program \texttt{genmake2} (located
521  in the \textit{tools} directory) to generate a Makefile.  in the \texttt{tools} directory) to generate a Makefile.
522  \texttt{genmake2} is a shell script written to work with all  \texttt{genmake2} is a shell script written to work with all
523  ``sh''--compatible shells including bash v1, bash v2, and Bourne.  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
524  Internally, \texttt{genmake2} determines the locations of needed  Internally, \texttt{genmake2} determines the locations of needed
525  files, the compiler, compiler options, libraries, and Unix tools.  It  files, the compiler, compiler options, libraries, and Unix tools.  It
526  relies upon a number of ``optfiles'' located in the {\em  relies upon a number of ``optfiles'' located in the
527    tools/build\_options} directory.  \texttt{tools/build\_options} directory.
528    
529  The purpose of the optfiles is to provide all the compilation options  The purpose of the optfiles is to provide all the compilation options
530  for particular ``platforms'' (where ``platform'' roughly means the  for particular ``platforms'' (where ``platform'' roughly means the
# Line 739  The most important command-line options Line 619  The most important command-line options
619    the user's path.  When these three items have been identified,    the user's path.  When these three items have been identified,
620    genmake2 will try to find an optfile that has a matching name.    genmake2 will try to find an optfile that has a matching name.
621        
622    \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
623      set of packages to be used.  The normal order of precedence for
624      packages is as follows:
625      \begin{enumerate}
626      \item If available, the command line (\texttt{--pdefault}) settings
627        over-rule any others.
628    
629      \item Next, \texttt{genmake2} will look for a file named
630        ``\texttt{packages.conf}'' in the local directory or in any of the
631        directories specified with the \texttt{--mods} option.
632        
633      \item Finally, if neither of the above are available,
634        \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
635      \end{enumerate}
636      
637  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
638    used for packages.    used for packages.
639        
# Line 751  The most important command-line options Line 646  The most important command-line options
646    assumed that the two packages are compatible and will function    assumed that the two packages are compatible and will function
647    either with or without each other.    either with or without each other.
648        
 \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default  
   set of packages to be used.  
     
   If not set, the default package list will be read from {\em  
     pkg/pkg\_default}  
     
649  \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or  \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
650    automatic differentiation options file to be used.  The file is    automatic differentiation options file to be used.  The file is
651    analogous to the ``optfile'' defined above but it specifies    analogous to the ``optfile'' defined above but it specifies
# Line 786  The most important command-line options Line 675  The most important command-line options
675      ``-standarddirs'' option)      ``-standarddirs'' option)
676    \end{itemize}    \end{itemize}
677        
678    \item[\texttt{--mpi}] This option enables certain MPI features (using
679      CPP \texttt{\#define}s) within the code and is necessary for MPI
680      builds (see Section \ref{sect:mpi-build}).
681      
682  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
683    soft-links and other bugs common with the \texttt{make} versions    soft-links and other bugs common with the \texttt{make} versions
684    provided by commercial Unix vendors, GNU \texttt{make} (sometimes    provided by commercial Unix vendors, GNU \texttt{make} (sometimes
685    called \texttt{gmake}) should be preferred.  This option provides a    called \texttt{gmake}) should be preferred.  This option provides a
686    means for specifying the make executable to be used.    means for specifying the make executable to be used.
687      
688    \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
689      machines, the ``bash'' shell is unavailable.  To run on these
690      systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
691      a Bourne, POSIX, or compatible) shell.  The syntax in these
692      circumstances is:
693      \begin{center}
694        \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
695      \end{center}
696      where \texttt{/bin/sh} can be replaced with the full path and name
697      of the desired shell.
698    
699  \end{description}  \end{description}
700    
701    
702    \subsection{Building with MPI}
703    \label{sect:mpi-build}
704    
705  \section{Running the model}  Building MITgcm to use MPI libraries can be complicated due to the
706  \label{sect:runModel}  variety of different MPI implementations available, their dependencies
707    or interactions with different compilers, and their often ad-hoc
708    locations within file systems.  For these reasons, its generally a
709    good idea to start by finding and reading the documentation for your
710    machine(s) and, if necessary, seeking help from your local systems
711    administrator.
712    
713    The steps for building MITgcm with MPI support are:
714    \begin{enumerate}
715      
716    \item Determine the locations of your MPI-enabled compiler and/or MPI
717      libraries and put them into an options file as described in Section
718      \ref{sect:genmake}.  One can start with one of the examples in:
719      \begin{rawhtml} <A
720        href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">
721      \end{rawhtml}
722      \begin{center}
723        \texttt{MITgcm/tools/build\_options/}
724      \end{center}
725      \begin{rawhtml} </A> \end{rawhtml}
726      such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
727      \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
728      hand.  You may need help from your user guide or local systems
729      administrator to determine the exact location of the MPI libraries.
730      If libraries are not installed, MPI implementations and related
731      tools are available including:
732      \begin{itemize}
733      \item \begin{rawhtml} <A
734          href="http://www-unix.mcs.anl.gov/mpi/mpich/">
735        \end{rawhtml}
736        MPICH
737        \begin{rawhtml} </A> \end{rawhtml}
738    
739      \item \begin{rawhtml} <A
740          href="http://www.lam-mpi.org/">
741        \end{rawhtml}
742        LAM/MPI
743        \begin{rawhtml} </A> \end{rawhtml}
744    
745      \item \begin{rawhtml} <A
746          href="http://www.osc.edu/~pw/mpiexec/">
747        \end{rawhtml}
748        MPIexec
749        \begin{rawhtml} </A> \end{rawhtml}
750      \end{itemize}
751      
752    \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
753      (see Section \ref{sect:genmake}) using commands such as:
754    {\footnotesize \begin{verbatim}
755      %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
756      %  make depend
757      %  make
758    \end{verbatim} }
759      
760    \item Run the code with the appropriate MPI ``run'' or ``exec''
761      program provided with your particular implementation of MPI.
762      Typical MPI packages such as MPICH will use something like:
763    \begin{verbatim}
764      %  mpirun -np 4 -machinefile mf ./mitgcmuv
765    \end{verbatim}
766      Sightly more complicated scripts may be needed for many machines
767      since execution of the code may be controlled by both the MPI
768      library and a job scheduling and queueing system such as PBS,
769      LoadLeveller, Condor, or any of a number of similar tools.  A few
770      example scripts (those used for our \begin{rawhtml} <A
771        href="http://mitgcm.org/testing.html"> \end{rawhtml}regular
772      verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
773      at:
774      \begin{rawhtml} <A
775        href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
776      \end{rawhtml}
777      {\footnotesize \tt
778        http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }
779      \begin{rawhtml} </A> \end{rawhtml}
780    
781    \end{enumerate}
782    
783  If compilation finished succesfuully (section \ref{sect:buildModel})  An example of the above process on the MITgcm cluster (``cg01'') using
784  then an executable called {\em mitgcmuv} will now exist in the local  the GNU g77 compiler and the mpich MPI library is:
 directory.  
785    
786  To run the model as a single process (ie. not in parallel) simply  {\footnotesize \begin{verbatim}
787  type:    %  cd MITgcm/verification/exp5
788      %  mkdir build
789      %  cd build
790      %  ../../../tools/genmake2 -mpi -mods=../code \
791           -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
792      %  make depend
793      %  make
794      %  cd ../input
795      %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
796           -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
797    \end{verbatim} }
798    
799    \section[Running MITgcm]{Running the model in prognostic mode}
800    \label{sect:runModel}
801    \begin{rawhtml}
802    <!-- CMIREDIR:runModel: -->
803    \end{rawhtml}
804    
805    If compilation finished succesfully (section \ref{sect:buildingCode})
806    then an executable called \texttt{mitgcmuv} will now exist in the
807    local directory.
808    
809    To run the model as a single process (\textit{ie.} not in parallel)
810    simply type:
811  \begin{verbatim}  \begin{verbatim}
812  % ./mitgcmuv  % ./mitgcmuv
813  \end{verbatim}  \end{verbatim}
# Line 814  do!). The above command will spew out ma Line 817  do!). The above command will spew out ma
817  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
818  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
819  etc. It is worth keeping this text output with the binary output so we  etc. It is worth keeping this text output with the binary output so we
820  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
821  \begin{verbatim}  \begin{verbatim}
822  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
823  \end{verbatim}  \end{verbatim}
824    In the event that the model encounters an error and stops, it is very
825  For the example experiments in {\em verification}, an example of the  helpful to include the last few line of this \texttt{output.txt} file
826  output is kept in {\em results/output.txt} for comparison. You can compare  along with the (\texttt{stderr}) error message within any bug reports.
827  your {\em output.txt} with this one to check that the set-up works.  
828    For the example experiments in \texttt{verification}, an example of the
829    output is kept in \texttt{results/output.txt} for comparison. You can
830    compare your \texttt{output.txt} with the corresponding one for that
831    experiment to check that the set-up works.
832    
833    
834    
835  \subsection{Output files}  \subsection{Output files}
836    
837  The model produces various output files. At a minimum, the instantaneous  The model produces various output files and, when using \texttt{mnc},
838  ``state'' of the model is written out, which is made of the following files:  sometimes even directories.  Depending upon the I/O package(s)
839    selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
840    both as determined by \texttt{code/packages.conf}) and the run-time
841    flags set (in \texttt{input/data.pkg}), the following output may
842    appear.
843    
844    
845    \subsubsection{MDSIO output files}
846    
847    The ``traditional'' output files are generated by the \texttt{mdsio}
848    package.  At a minimum, the instantaneous ``state'' of the model is
849    written out, which is made of the following files:
850    
851  \begin{itemize}  \begin{itemize}
852  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
853  0 $ eastward).    and positive eastward).
854    
855  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
856  and $> 0$ northward).    (m/s and positive northward).
857    
858  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
859  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
860  i.e. downward).    towards increasing pressure i.e. downward).
861    
862  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
863  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
864    
865  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
866  (g/kg).    vapor (g/kg).
867    
868  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
869  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
870  \end{itemize}  \end{itemize}
871    
872  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
873  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
874  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
875    
876  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
877    
878  \begin{itemize}  \begin{itemize}
879  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
880  \end{itemize}  \end{itemize}
881    
882  is written out. This file represents the state of the model in a condensed  is written out. This file represents the state of the model in a condensed
# Line 866  form and is used for restarting the inte Line 884  form and is used for restarting the inte
884  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
885    
886  \begin{itemize}  \begin{itemize}
887  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
888  \end{itemize}  \end{itemize}
889    
890  containing the D-grid velocity data and that has to be written out as well  containing the D-grid velocity data and that has to be written out as well
891  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
892  as the pickup files but are named differently. Their name contain the chain  as the pickup files but are named differently. Their name contain the chain
893  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
894  used to restart the model but are overwritten every other time they are  used to restart the model but are overwritten every other time they are
895  output to save disk space during long integrations.  output to save disk space during long integrations.
896    
897    \subsubsection{MNC output files}
898    
899    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
900    is usually (though not necessarily) placed within a subdirectory with
901    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  
902    
903  \subsection{Looking at the output}  \subsection{Looking at the output}
904    
905  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
906  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
907  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \texttt{.data} and \texttt{.meta}. The
908  binary form (big\_endian by default). The \textit{.meta} file is a  \texttt{.data} file contains the data written in binary form
909  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
910  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
911  particularly useful when running multi-processors calculations. The base  \texttt{.data} file. This way of organizing the output is particularly
912  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
913  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
914  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
915  the data. Look at the comments inside the script to see how to use it.  \texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m}
916    reads the data. Look at the comments inside the script to see how to
917    use it.
918    
919  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
920  \begin{verbatim}  \begin{verbatim}
# Line 905  Some examples of reading and visualizing Line 931  Some examples of reading and visualizing
931  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
932  \end{verbatim}  \end{verbatim}
933    
934  \section{Doing it yourself: customizing the code}  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
935    they are described in Section \ref{sec:pkg:mnc}.
 When you are ready to run the model in the configuration you want, the  
 easiest thing is to use and adapt the setup of the case studies  
 experiment (described previously) that is the closest to your  
 configuration. Then, the amount of setup will be minimized. In this  
 section, we focus on the setup relative to the ``numerical model''  
 part of the code (the setup relative to the ``execution environment''  
 part is covered in the parallel implementation section) and on the  
 variables and parameters that you are likely to change.  
   
 \subsection{Configuration and setup}  
   
 The CPP keys relative to the ``numerical model'' part of the code are  
 all defined and set in the file \textit{CPP\_OPTIONS.h }in the  
 directory \textit{ model/inc }or in one of the \textit{code  
 }directories of the case study experiments under  
 \textit{verification.} The model parameters are defined and declared  
 in the file \textit{model/inc/PARAMS.h }and their default values are  
 set in the routine \textit{model/src/set\_defaults.F. }The default  
 values can be modified in the namelist file \textit{data }which needs  
 to be located in the directory where you will run the model. The  
 parameters are initialized in the routine  
 \textit{model/src/ini\_parms.F}.  Look at this routine to see in what  
 part of the namelist the parameters are located.  
   
 In what follows the parameters are grouped into categories related to  
 the computational domain, the equations solved in the model, and the  
 simulation controls.  
   
 \subsection{Computational domain, geometry and time-discretization}  
   
 \begin{description}  
 \item[dimensions] \  
     
   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.)  
   
 \item[grid] \  
     
   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.  
   
 \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}\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...)  
   
 \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}\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{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}\textit{\ }and  
   \textbf{ meridWindFile }corresponding to the zonal and meridional  
   components of the wind stress, respectively (if you want the stress  
   to be along the direction of only one of the model horizontal axes,  
   you only need to generate one file). The format of the files is  
   similar to the bathymetry file. The zonal (meridional) stress data  
   are assumed to be in Pa and located at U-points (V-points). As for  
   the bathymetry, the precision with which to read the binary data is  
   controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } See  
   the matlab program \textit{gendata.m }in the \textit{input  
   }directories under \textit{verification }to see how simple  
   analytical wind forcing data are generated for the case study  
   experiments.  
     
   There is also the possibility of prescribing time-dependent periodic  
   forcing. To do this, concatenate the successive time records into a  
   single file (for each stress component) ordered in a (x, y, t)  
   fashion and set the following variables:  
   \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',  
   \textbf{externForcingPeriod }to the period (in s) of which the  
   forcing varies (typically 1 month), and \textbf{externForcingCycle  
   }to the repeat time (in s) of the forcing (typically 1 year -- note:  
   \textbf{ externForcingCycle }must be a multiple of  
   \textbf{externForcingPeriod}).  With these variables set up, the  
   model will interpolate the forcing linearly at each iteration.  
   
 \item[dissipation] \  
     
   The lateral eddy viscosity coefficient is specified through the  
   variable \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The  
   vertical eddy viscosity coefficient is specified through the  
   variable \textbf{viscAz }(in m$^{2}$s$ ^{-1}$) for the ocean and  
   \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) for the atmosphere.  
   The vertical diffusive fluxes can be computed implicitly by setting  
   the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}  
   .'. In addition, biharmonic mixing can be added as well through the  
   variable \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a  
   spherical polar grid, you might also need to set the variable  
   \textbf{cosPower} which is set to 0 by default and which represents  
   the power of cosine of latitude to multiply viscosity. Slip or  
   no-slip conditions at lateral and bottom boundaries are specified  
   through the logical variables \textbf{no\_slip\_sides}\textit{\ }  
   and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}',  
   free-slip boundary conditions are applied. If no-slip boundary  
   conditions are applied at the bottom, a bottom drag can be applied  
   as well. Two forms are available: linear (set the variable  
   \textbf{bottomDragLinear}\textit{\ }in s$ ^{-1}$) and quadratic (set  
   the variable \textbf{bottomDragQuadratic}\textit{ \ }in m$^{-1}$).  
   
   The Fourier and Shapiro filters are described elsewhere.  
   
 \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}\textit{\ }and \textbf{cg2dTargetResidual } for  
   the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{  
     cg3dTargetResidual }for the 3D case. You probably won't need to  
   alter the default values (are we sure of this?).  
     
   For the calculation of the surface pressure (for the ocean) or  
   surface geopotential (for the atmosphere) you need to set the  
   logical variables \textbf{rigidLid} and  
   \textbf{implicitFreeSurface}\textit{\ }(set one to '.  
   \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how  
   you want to deal with the ocean upper or atmosphere lower boundary).  
   
 \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}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{  
 tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off  
 terms in the temperature equation (same thing for salinity or specific  
 humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{  
 saltAdvection}\textit{\ }etc). These variables are all assumed here to be  
 set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a  
 precise definition.  
936    
937  \begin{description}  The MNC output files are all in the ``self-describing'' netCDF
938  \item[initialization] \  format and can thus be browsed and/or plotted using tools such as:
939      \begin{itemize}
940    The initial tracer data can be contained in the binary files  \item \texttt{ncdump} is a utility which is typically included
941    \textbf{ hydrogThetaFile }and \textbf{hydrogSaltFile}. These files    with every netCDF install:
942    should contain 3D data ordered in an (x, y, r) fashion with k=1 as    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
943    the first vertical level.  If no file names are provided, the  \begin{verbatim}
944    tracers are then initialized with the values of \textbf{tRef }and  http://www.unidata.ucar.edu/packages/netcdf/
945    \textbf{sRef }mentioned above (in the equation of state section). In  \end{verbatim}
946    this case, the initial tracer data are uniform in x and y for each    \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
947    depth level.    binaries into formatted ASCII text files.
   
 \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}\textit{. }  Alternatively or in addition, the  
   forcing can be specified through a relaxation term. The SST data to  
   which the model surface temperatures are restored to are supposed to  
   be stored in the 2D binary file \textbf{ thetaClimFile}\textit{.  
   }The corresponding relaxation time scale coefficient is set through  
   the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The same  
   procedure applies for salinity with the variable names  
   \textbf{EmPmRfile }\textit{, }\textbf{saltClimFile}\textit{, }and  
   \textbf{tauSaltClimRelax} \textit{\ }for freshwater flux (in m/s)  
   and surface salinity (in ppt) data files and relaxation time scale  
   coefficient (in s), respectively. Also for salinity, if the CPP key  
   \textbf{USE\_NATURAL\_BCS} is turned on, natural boundary conditions  
   are applied i.e. when computing the surface salinity tendency, the  
   freshwater flux is multiplied by the model surface salinity instead  
   of a constant salinity value.  
     
   As for the other input files, the precision with which to read the  
   data is controlled by the variable \textbf{readBinaryPrec}.  
   Time-dependent, periodic forcing can be applied as well following  
   the same procedure used for the wind forcing data (see above).  
   
 \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).  
948    
949  \begin{description}  \item \texttt{ncview} utility is a very convenient and quick way
950  \item[run duration] \    to plot netCDF data and it runs on most OSes:
951      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
952    \begin{verbatim}
953    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
954    \end{verbatim}
955      \begin{rawhtml} </A> \end{rawhtml}
956        
957    The beginning of a simulation is set by specifying a start time (in  \item MatLAB(c) and other common post-processing environments provide
958    s) through the real variable \textbf{startTime }or by specifying an    various netCDF interfaces including:
959    initial iteration number through the integer variable    \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
960    \textbf{nIter0}. If these variables are set to nonzero values, the  \begin{verbatim}
961    model will look for a ''pickup'' file \textit{pickup.0000nIter0 }to  http://mexcdf.sourceforge.net/
962    restart the integration\textit{. }The end of a simulation is set  \end{verbatim}
963    through the real variable \textbf{endTime }(in s).  Alternatively,    \begin{rawhtml} </A> \end{rawhtml}
964    you can specify instead the number of time steps to execute through    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
965    the integer variable \textbf{nTimeSteps}.  \begin{verbatim}
966    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
967  \item[frequency of output] \  \end{verbatim}
968        \begin{rawhtml} </A> \end{rawhtml}
969    Real variables defining frequencies (in s) with which output files  \end{itemize}
   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}  
   
970    
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