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# Line 3  Line 3 
3    
4  %\section{Getting started}  %\section{Getting started}
5    
6  In this section, we describe how to use the model. In the first  We believe the best way to familiarize yourself with the
 section, we provide enough information to help you get started with  
 the model. We believe the best way to familiarize yourself with the  
7  model is to run the case study examples provided with the base  model is to run the case study examples provided with the base
8  version. Information on how to obtain, compile, and run the code is  version. Information on how to obtain, compile, and run the code is
9  found there as well as a brief description of the model structure  found here as well as a brief description of the model structure
10  directory and the case study examples.  The latter and the code  directory and the case study examples. Information is also provided
11  structure are described more fully in chapters  here on how to customize the code when you are ready to try implementing
12  \ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in  the configuration you have in mind.  The code and algorithm
13  this section, we provide information on how to customize the code when  are described more fully in chapters \ref{chap:discretization} and
14  you are ready to try implementing the configuration you have in mind.  \ref{chap:sarch}.
15    
16  \section{Where to find information}  \section{Where to find information}
17  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
18    \begin{rawhtml}
19    <!-- CMIREDIR:whereToFindInfo: -->
20    \end{rawhtml}
21    
22  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  
23  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
24  \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}
25  \begin{verbatim}  \begin{verbatim}
# Line 37  http://mitgcm.org/mailman/listinfo/mitgc Line 27  http://mitgcm.org/mailman/listinfo/mitgc
27  http://mitgcm.org/pipermail/mitgcm-support/  http://mitgcm.org/pipermail/mitgcm-support/
28  \end{verbatim}  \end{verbatim}
29  \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  
   
   
30    
31  \section{Obtaining the code}  \section{Obtaining the code}
32  \label{sect:obtainingCode}  \label{sect:obtainingCode}
33    \begin{rawhtml}
34    <!-- CMIREDIR:obtainingCode: -->
35    \end{rawhtml}
36    
37  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
38  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 92  be set within your shell.  For a csh or Line 75  be set within your shell.  For a csh or
75  \begin{verbatim}  \begin{verbatim}
76  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
77  \end{verbatim}  \end{verbatim}
78  in your .cshrc or .tcshrc file.  For bash or sh shells, put:  in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
79    shells, put:
80  \begin{verbatim}  \begin{verbatim}
81  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
82  \end{verbatim}  \end{verbatim}
# Line 118  The MITgcm web site contains further dir Line 102  The MITgcm web site contains further dir
102  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
103  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
104  development milestones:  development milestones:
105  \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
106  \begin{verbatim}  \begin{verbatim}
107  http://mitgcm.org/source_code.html  http://mitgcm.org/source_code.html
108  \end{verbatim}  \end{verbatim}
# Line 147  of CVS aliases Line 131  of CVS aliases
131    \label{tab:cvsModules}    \label{tab:cvsModules}
132  \end{table}  \end{table}
133    
134  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \texttt{MITgcm}. If
135  the directory \textit{MITgcm} exists this command updates your code  the directory \texttt{MITgcm} exists this command updates your code
136  based on the repository. Each directory in the source tree contains a  based on the repository. Each directory in the source tree contains a
137  directory \textit{CVS}. This information is required by CVS to keep  directory \texttt{CVS}. This information is required by CVS to keep
138  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
139  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
140  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
141  MITgcm code can be found  MITgcm code can be found
142  \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}
143  here  here
144  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
145  .  .
# Line 168  they create can be changed to a differen Line 152  they create can be changed to a differen
152     %  mv MITgcm MITgcm_verif_basic     %  mv MITgcm MITgcm_verif_basic
153  \end{verbatim}  \end{verbatim}
154    
   
 \subsection{Method 2 - Tar file download}  
 \label{sect:conventionalDownload}  
   
 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}  
 \begin{verbatim}  
 http://mitgcm.org/download/  
 \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.  
   
155  \subsubsection{Upgrading from an earlier version}  \subsubsection{Upgrading from an earlier version}
156    
157  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''
# Line 255  that you may only have part of a patch. Line 218  that you may only have part of a patch.
218  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
219  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
220    
221    \subsection{Method 2 - Tar file download}
222    \label{sect:conventionalDownload}
223    
224    If you do not have CVS on your system, you can download the model as a
225    tar file from the web site at:
226    \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
227    \begin{verbatim}
228    http://mitgcm.org/download/
229    \end{verbatim}
230    \begin{rawhtml} </A> \end{rawhtml}
231    The tar file still contains CVS information which we urge you not to
232    delete; even if you do not use CVS yourself the information can help
233    us if you should need to send us your copy of the code.  If a recent
234    tar file does not exist, then please contact the developers through
235    the
236    \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
237    MITgcm-support@mitgcm.org
238    \begin{rawhtml} </A> \end{rawhtml}
239    mailing list.
240    
241  \section{Model and directory structure}  \section{Model and directory structure}
242    \begin{rawhtml}
243    <!-- CMIREDIR:directory_structure: -->
244    \end{rawhtml}
245    
246  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
247  support wrapper. This wrapper is designed to provide a general  support wrapper. This wrapper is designed to provide a general
# Line 263  framework for grid-point models. MITgcmU Line 249  framework for grid-point models. MITgcmU
249  model that uses the framework. Under this structure the model is split  model that uses the framework. Under this structure the model is split
250  into execution environment support code and conventional numerical  into execution environment support code and conventional numerical
251  model code. The execution environment support code is held under the  model code. The execution environment support code is held under the
252  \textit{eesupp} directory. The grid point model code is held under the  \texttt{eesupp} directory. The grid point model code is held under the
253  \textit{model} directory. Code execution actually starts in the  \texttt{model} directory. Code execution actually starts in the
254  \textit{eesupp} routines and not in the \textit{model} routines. For  \texttt{eesupp} routines and not in the \texttt{model} routines. For
255  this reason the top-level \textit{MAIN.F} is in the  this reason the top-level \texttt{MAIN.F} is in the
256  \textit{eesupp/src} directory. In general, end-users should not need  \texttt{eesupp/src} directory. In general, end-users should not need
257  to worry about this level. The top-level routine for the numerical  to worry about this level. The top-level routine for the numerical
258  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
259  a brief description of the directory structure of the model under the  a brief description of the directory structure of the model under the
260  root tree (a detailed description is given in section 3: Code  root tree (a detailed description is given in section 3: Code
261  structure).  structure).
262    
263  \begin{itemize}  \begin{itemize}
264    
265  \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}.  
266        
267  \item \textit{exe}: this directory is initially empty. It is the  \item \texttt{eesupp}: contains the execution environment source code.
268    default directory in which to execute the code.    Also subdivided into two subdirectories \texttt{inc} and
269      \texttt{src}.
270      
271    \item \texttt{model}: this directory contains the main source code.
272      Also subdivided into two subdirectories \texttt{inc} and
273      \texttt{src}.
274        
275  \item \textit{model}: this directory contains the main source code.  \item \texttt{pkg}: contains the source code for the packages. Each
276    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}  
277    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
278    \textit{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
279    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in chapter \ref{chap.packagesI}.
280        
281  \item \textit{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
282    For example, \textit{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
283    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
284    \textit{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
285    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
286    The latter is described in details in part V.    The latter is described in detail in part \ref{chap.ecco}.
287      This directory also contains the subdirectory build\_options, which
288      contains the `optfiles' with the compiler options for the different
289      compilers and machines that can run MITgcm.
290        
291  \item \textit{utils}: this directory contains various utilities. The  \item \texttt{utils}: this directory contains various utilities. The
292    subdirectory \textit{knudsen2} contains code and a makefile that    subdirectory \texttt{knudsen2} contains code and a makefile that
293    compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
294    formula for an ocean nonlinear equation of state. The    formula for an ocean nonlinear equation of state. The
295    \textit{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
296    model output directly into matlab. \textit{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
297    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
298    model output.    model output. The subdirectory exch2 contains the code needed for
299      the exch2 package to work with different combinations of domain
300      decompositions.
301        
302  \item \textit{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
303    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sect:modelExamples}.
304    
305  \end{itemize}  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
   
 \section[MITgcm Example Experiments]{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}.  
306        
307  \item \textit{exp2} - 4x4 degree global ocean simulation with steady  \item \texttt{lsopt}: Line search code used for optimization.
   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{optim}: Interface between MITgcm and line search code.
   scheme; 1 month integration  
310        
 \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.  
311  \end{itemize}  \end{itemize}
312    
 Once you have chosen the example you want to run, you are ready to  
 compile the code.  
   
313  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
314  \label{sect:buildingCode}  \label{sect:buildingCode}
315    \begin{rawhtml}
316  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
317  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
318  compiler and optimization options and also figures out any file  
319  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
320  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
321    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
322    file dependencies. We supply a script (\texttt{genmake2}), described
323    in section \ref{sect:genmake}, that automatically creates the
324    \texttt{Makefile} for you. You then need to build the dependencies and
325  compile the code.  compile the code.
326    
327  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
328  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
329  actually do this but here let's build the code in  actually do this but here let's build the code in
330  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
331  \begin{verbatim}  \begin{verbatim}
332  % cd verification/exp2/input  % cd verification/exp2/build
333  \end{verbatim}  \end{verbatim}
334  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
335  \begin{verbatim}  \begin{verbatim}
336  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
337  \end{verbatim}  \end{verbatim}
338  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
339  code with any files in the directory {\em ./code/}.  code with any files in the directory \texttt{../code/}.
340    
341  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
342  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
343  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
344  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
345    tools/build\_options} directory.  Under some circumstances, a user  the \texttt{tools/build\_options} directory.  Under some
346  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
347  combination of compiler, compiler flags, libraries, and other options  specify the exact combination of compiler, compiler flags, libraries,
348  necessary to build a particular configuration of MITgcm.  In such  and other options necessary to build a particular configuration of
349  cases, it is generally helpful to read the existing ``optfiles'' and  MITgcm.  In such cases, it is generally helpful to read the existing
350  mimic their syntax.  ``optfiles'' and mimic their syntax.
351    
352  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
353  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
354  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
355  architectures) to the  architectures) to the
356  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
357  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
358  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
359  list.  list.
360    
361  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
362  \begin{verbatim}  \begin{verbatim}
363  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
364  \end{verbatim}  \end{verbatim}
365    
366  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
367    dependencies with the command:
368  \begin{verbatim}  \begin{verbatim}
369  % make depend  % make depend
370  \end{verbatim}  \end{verbatim}
371  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
372  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
373  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
374    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
375  directory.  this directory.  It is important to note that the {\tt make depend}
376    stage will occasionally produce warnings or errors since the
377    dependency parsing tool is unable to find all of the necessary header
378    files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
379    is usually OK to ignore the warnings/errors and proceed to the next
380    step.
381    
382  Next compile the code:  Next one can compile the code using:
383  \begin{verbatim}  \begin{verbatim}
384  % make  % make
385  \end{verbatim}  \end{verbatim}
386  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
387  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
388  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
389    (shared multi-processor) systems, the build process can often be sped
390    up appreciably using the command:
391    \begin{verbatim}
392    % make -j 2
393    \end{verbatim}
394    where the ``2'' can be replaced with a number that corresponds to the
395    number of CPUs available.
396    
397  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
398  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
399    first creating links to all the input files:
400    \begin{verbatim}
401    ln -s ../input/* .
402    \end{verbatim}
403    and then calling the executable with:
404  \begin{verbatim}  \begin{verbatim}
405  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
406  \end{verbatim}  \end{verbatim}
407  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
408  output.txt}.  \texttt{output.txt}.
   
409    
410  \subsection{Building/compiling the code elsewhere}  \subsection{Building/compiling the code elsewhere}
411    
# Line 948  the GNU g77 compiler and the mpich MPI l Line 794  the GNU g77 compiler and the mpich MPI l
794         -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv         -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
795  \end{verbatim} }  \end{verbatim} }
796    
   
   
797  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
798  \label{sect:runModel}  \label{sect:runModel}
799    \begin{rawhtml}
800    <!-- CMIREDIR:runModel: -->
801    \end{rawhtml}
802    
803  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sect:buildingCode})
804  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
805  local directory.  local directory.
806    
807  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)
808  type:  simply type:
809  \begin{verbatim}  \begin{verbatim}
810  % ./mitgcmuv  % ./mitgcmuv
811  \end{verbatim}  \end{verbatim}
# Line 968  do!). The above command will spew out ma Line 815  do!). The above command will spew out ma
815  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
816  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
817  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
818  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
819  \begin{verbatim}  \begin{verbatim}
820  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
821  \end{verbatim}  \end{verbatim}
822    In the event that the model encounters an error and stops, it is very
823  For the example experiments in {\em verification}, an example of the  helpful to include the last few line of this \texttt{output.txt} file
824  output is kept in {\em results/output.txt} for comparison. You can compare  along with the (\texttt{stderr}) error message within any bug reports.
825  your {\em output.txt} with this one to check that the set-up works.  
826    For the example experiments in \texttt{verification}, an example of the
827    output is kept in \texttt{results/output.txt} for comparison. You can
828    compare your \texttt{output.txt} with the corresponding one for that
829    experiment to check that the set-up works.
830    
831    
832    
833  \subsection{Output files}  \subsection{Output files}
834    
835  The model produces various output files. At a minimum, the instantaneous  The model produces various output files and, when using \texttt{mnc},
836  ``state'' of the model is written out, which is made of the following files:  sometimes even directories.  Depending upon the I/O package(s)
837    selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
838    both as determined by \texttt{code/packages.conf}) and the run-time
839    flags set (in \texttt{input/data.pkg}), the following output may
840    appear.
841    
842    
843    \subsubsection{MDSIO output files}
844    
845    The ``traditional'' output files are generated by the \texttt{mdsio}
846    package.  At a minimum, the instantaneous ``state'' of the model is
847    written out, which is made of the following files:
848    
849  \begin{itemize}  \begin{itemize}
850  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
851  0 $ eastward).    and positive eastward).
852    
853  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
854  and $> 0$ northward).    (m/s and positive northward).
855    
856  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
857  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
858  i.e. downward).    towards increasing pressure i.e. downward).
859    
860  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
861  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
862    
863  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
864  (g/kg).    vapor (g/kg).
865    
866  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
867  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
868  \end{itemize}  \end{itemize}
869    
870  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
871  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
872  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
873    
874  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
875    
876  \begin{itemize}  \begin{itemize}
877  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
878  \end{itemize}  \end{itemize}
879    
880  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 1020  form and is used for restarting the inte Line 882  form and is used for restarting the inte
882  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
883    
884  \begin{itemize}  \begin{itemize}
885  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
886  \end{itemize}  \end{itemize}
887    
888  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
889  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
890  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
891  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
892  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
893  output to save disk space during long integrations.  output to save disk space during long integrations.
894    
895    \subsubsection{MNC output files}
896    
897    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
898    is usually (though not necessarily) placed within a subdirectory with
899    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  
900    
901  \subsection{Looking at the output}  \subsection{Looking at the output}
902    
903  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
904  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
905  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \texttt{.data} and \texttt{.meta}. The
906  binary form (big\_endian by default). The \textit{.meta} file is a  \texttt{.data} file contains the data written in binary form
907  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
908  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
909  particularly useful when running multi-processors calculations. The base  \texttt{.data} file. This way of organizing the output is particularly
910  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
911  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
912  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
913  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}
914    reads the data. Look at the comments inside the script to see how to
915    use it.
916    
917  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
918  \begin{verbatim}  \begin{verbatim}
# Line 1059  Some examples of reading and visualizing Line 929  Some examples of reading and visualizing
929  >> 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
930  \end{verbatim}  \end{verbatim}
931    
932    Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
933    they are described in Section \ref{sec:pkg:mnc}.
934    
935    The MNC output files are all in the ``self-describing'' netCDF
936    format and can thus be browsed and/or plotted using tools such as:
937    \begin{itemize}
938    \item \texttt{ncdump} is a utility which is typically included
939      with every netCDF install:
940      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
941    \begin{verbatim}
942    http://www.unidata.ucar.edu/packages/netcdf/
943    \end{verbatim}
944      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
945      binaries into formatted ASCII text files.
946    
947    \item \texttt{ncview} utility is a very convenient and quick way
948      to plot netCDF data and it runs on most OSes:
949      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
950    \begin{verbatim}
951    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
952    \end{verbatim}
953      \begin{rawhtml} </A> \end{rawhtml}
954      
955    \item MatLAB(c) and other common post-processing environments provide
956      various netCDF interfaces including:
957      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
958    \begin{verbatim}
959    http://mexcdf.sourceforge.net/
960    \end{verbatim}
961      \begin{rawhtml} </A> \end{rawhtml}
962      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
963    \begin{verbatim}
964    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
965    \end{verbatim}
966      \begin{rawhtml} </A> \end{rawhtml}
967    \end{itemize}
968    
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