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revision 1.30 by edhill, Sat Oct 16 03:40:13 2004 UTC revision 1.37 by molod, Wed Jun 28 16:48:19 2006 UTC
# Line 15  structure are described more fully in ch Line 15  structure are described more fully in ch
15  this section, we provide information on how to customize the code when  this section, we provide information on how to customize the code when
16  you are ready to try implementing the configuration you have in mind.  you are ready to try implementing the configuration you have in mind.
17    
   
18  \section{Where to find information}  \section{Where to find information}
19  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
20  \begin{rawhtml}  \begin{rawhtml}
21  <!-- CMIREDIR:whereToFindInfo: -->  <!-- CMIREDIR:whereToFindInfo: -->
22  \end{rawhtml}  \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 41  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}
# Line 99  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}
# Line 125  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}
# Line 154  of CVS aliases Line 133  of CVS aliases
133    \label{tab:cvsModules}    \label{tab:cvsModules}
134  \end{table}  \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  .  .
# Line 175  they create can be changed to a differen Line 154  they create can be changed to a differen
154     %  mv MITgcm MITgcm_verif_basic     %  mv MITgcm MITgcm_verif_basic
155  \end{verbatim}  \end{verbatim}
156    
   
 \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.  
   
157  \subsubsection{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''
# Line 262  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}  \begin{rawhtml}
245  <!-- CMIREDIR:directory_structure: -->  <!-- CMIREDIR:directory_structure: -->
# Line 273  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.  
268        
269  \item \textit{diags}: contains the code relative to time-averaged  \item \texttt{eesupp}: contains the execution environment source code.
270    diagnostics. It is subdivided into two subdirectories \textit{inc}    Also subdivided into two subdirectories \texttt{inc} and
271    and \textit{src} that contain include files (*.\textit{h} files) and    \texttt{src}.
272    Fortran subroutines (*.\textit{F} files), respectively.    
273    \item \texttt{model}: this directory contains the main source code.
274  \item \textit{doc}: contains brief documentation notes.    Also subdivided into two subdirectories \texttt{inc} and
275      \texttt{src}.
276        
277  \item \textit{eesupp}: contains the execution environment 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{exe}: this directory is initially empty. It is the  
   default directory in which to execute the code.  
     
 \item \textit{model}: this directory contains the main source code.  
   Also subdivided into two subdirectories \textit{inc} and  
   \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[MITgcm Example Experiments]{Example experiments}  
 \label{sect:modelExamples}  
 \begin{rawhtml}  
 <!-- CMIREDIR:modelExamples: -->  
 \end{rawhtml}  
   
 %% a set of twenty-four pre-configured numerical experiments  
   
 The MITgcm distribution comes with more than a dozen pre-configured  
 numerical experiments. Some of these example experiments are tests of  
 individual parts of the model code, but many are fully fledged  
 numerical simulations. A few of the examples are used for tutorial  
 documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.  
 The other examples follow the same general structure as the tutorial  
 examples. However, they only include brief instructions in a text file  
 called {\it README}.  The examples are located in subdirectories under  
 the directory \textit{verification}. Each example is briefly described  
 below.  
   
 \subsection{Full list of model examples}  
   
 \begin{enumerate}  
     
 \item \textit{exp0} - single layer, ocean double gyre (barotropic with  
   free-surface). This experiment is described in detail in section  
   \ref{sect:eg-baro}.  
   
 \item \textit{exp1} - Four layer, ocean double gyre. This experiment  
   is described in detail in section \ref{sect:eg-baroc}.  
     
 \item \textit{exp2} - 4x4 degree global ocean simulation with steady  
   climatological forcing. This experiment is described in detail in  
   section \ref{sect:eg-global}.  
     
 \item \textit{exp4} - Flow over a Gaussian bump in open-water or  
   channel with open boundaries.  
     
 \item \textit{exp5} - Inhomogenously forced ocean convection in a  
   doubly periodic box.  
   
 \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for  
 Gent/McWilliams scheme). 2D (Y-Z).  
   
 \item \textit{internal wave} - Ocean internal wave forced by open  
   boundary conditions.  
     
 \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  
   scheme; 1 month integration  
     
 \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and  
   Suarez '94 forcing.  
     
 \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing.  
     
 \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing on the cubed sphere.  
     
 \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  
   Global Zonal Mean configuration, 1x64x5 resolution.  
     
 \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate  
   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).  
     
 \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  
   physics. 3D Equatorial Channel configuration.  
     
 \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.  
   Global configuration, on latitude longitude grid with 128x64x5 grid  
   points ($2.8^\circ{\rm degree}$ resolution).  
     
 \item \textit{adjustment.128x64x1} Barotropic adjustment problem on  
   latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on  
   cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \textit{advect\_cs} Two-dimensional passive advection test on  
   cube sphere grid.  
     
 \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive  
   advection test on Cartesian grid.  
     
 \item \textit{advect\_yz} Two-dimensional (vertical plane) passive  
   advection test on Cartesian grid.  
     
 \item \textit{carbon} Simple passive tracer experiment. Includes  
   derivative calculation. Described in detail in section  
   \ref{sect:eg-carbon-ad}.  
   
 \item \textit{flt\_example} Example of using float package.  
     
 \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux  
   boundary conditions and poles.  
   
 \item \textit{global\_ocean\_pressure} Global circulation in pressure  
   coordinate (non-Boussinesq ocean model). Described in detail in  
   section \ref{sect:eg-globalpressure}.  
     
 \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube  
   sphere grid.  
   
 \end{enumerate}  
   
 \subsection{Directory structure of model examples}  
   
 Each example directory has the following subdirectories:  
   
 \begin{itemize}  
 \item \textit{code}: contains the code particular to the example. At a  
   minimum, this directory includes the following files:  
   
   \begin{itemize}  
   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to  
     the ``execution environment'' part of the code. The default  
     version is located in \textit{eesupp/inc}.  
     
   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to  
     the ``numerical model'' part of the code. The default version is  
     located in \textit{model/inc}.  
     
   \item \textit{code/SIZE.h}: declares size of underlying  
     computational grid.  The default version is located in  
     \textit{model/inc}.  
   \end{itemize}  
     
   In addition, other include files and subroutines might be present in  
   \textit{code} depending on the particular experiment. See Section 2  
   for more details.  
     
 \item \textit{input}: contains the input data files required to run  
   the example. At a minimum, the \textit{input} directory contains the  
   following files:  
   
   \begin{itemize}  
   \item \textit{input/data}: this file, written as a namelist,  
     specifies the main parameters for the experiment.  
308        
309    \item \textit{input/data.pkg}: contains parameters relative to the  \item \texttt{lsopt}: Line search code used for optimization.
     packages used in the experiment.  
310        
311    \item \textit{input/eedata}: this file contains ``execution  \item \texttt{optim}: Interface between MITgcm and line search code.
     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}  
312        
   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    
 Once you have chosen the example you want to run, you are ready to  
 compile the code.  
   
315  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
316  \label{sect:buildingCode}  \label{sect:buildingCode}
317  \begin{rawhtml}  \begin{rawhtml}
318  <!-- CMIREDIR:buildingCode: -->  <!-- CMIREDIR:buildingCode: -->
319  \end{rawhtml}  \end{rawhtml}
320    
321  To compile the code, we use the {\em make} program. This uses a file  To compile the code, we use the \texttt{make} program. This uses a
322  ({\em Makefile}) that allows us to pre-process source files, specify  file (\texttt{Makefile}) that allows us to pre-process source files,
323  compiler and optimization options and also figures out any file  specify compiler and optimization options and also figures out any
324  dependencies. We supply a script ({\em genmake2}), described in  file dependencies. We supply a script (\texttt{genmake2}), described
325  section \ref{sect:genmake}, that automatically creates the {\em  in section \ref{sect:genmake}, that automatically creates the
326    Makefile} for you. You then need to build the dependencies and  \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 (``optfiles'') contained in  appropriate set of options from the files (``optfiles'') contained in
347  the {\em tools/build\_options} directory.  Under some circumstances, a  the \texttt{tools/build\_options} directory.  Under some
348  user may have to create a new ``optfile'' in order to specify the  circumstances, a user may have to create a new ``optfile'' in order to
349  exact combination of compiler, compiler flags, libraries, and other  specify the exact combination of compiler, compiler flags, libraries,
350  options necessary to build a particular configuration of MITgcm.  In  and other options necessary to build a particular configuration of
351  such cases, it is generally helpful to read the existing ``optfiles''  MITgcm.  In such cases, it is generally helpful to read the existing
352  and 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.  It is important to note that the {\tt make depend} stage  this directory.  It is important to note that the {\tt make depend}
378  will occasionally produce warnings or errors since the dependency  stage will occasionally produce warnings or errors since the
379  parsing tool is unable to find all of the necessary header files  dependency parsing tool is unable to find all of the necessary header
380  (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it is  files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
381  usually OK to ignore the warnings/errors and proceed to the next step.  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}
413    
414    In the example above (section \ref{sect:buildingCode}) we built the
415    executable in the {\em input} directory of the experiment for
416    convenience. You can also configure and compile the code in other
417    locations, for example on a scratch disk with out having to copy the
418    entire source tree. The only requirement to do so is you have {\tt
419      genmake2} in your path or you know the absolute path to {\tt
420      genmake2}.
421    
422    The following sections outline some possible methods of organizing
423    your source and data.
424    
425    \subsubsection{Building from the {\em ../code directory}}
426    
427    This is just as simple as building in the {\em input/} directory:
428    \begin{verbatim}
429    % cd verification/exp2/code
430    % ../../../tools/genmake2
431    % make depend
432    % make
433    \end{verbatim}
434    However, to run the model the executable ({\em mitgcmuv}) and input
435    files must be in the same place. If you only have one calculation to make:
436    \begin{verbatim}
437    % cd ../input
438    % cp ../code/mitgcmuv ./
439    % ./mitgcmuv > output.txt
440    \end{verbatim}
441    or if you will be making multiple runs with the same executable:
442    \begin{verbatim}
443    % cd ../
444    % cp -r input run1
445    % cp code/mitgcmuv run1
446    % cd run1
447    % ./mitgcmuv > output.txt
448    \end{verbatim}
449    
450    \subsubsection{Building from a new directory}
451    
452    Since the {\em input} directory contains input files it is often more
453    useful to keep {\em input} pristine and build in a new directory
454    within {\em verification/exp2/}:
455    \begin{verbatim}
456    % cd verification/exp2
457    % mkdir build
458    % cd build
459    % ../../../tools/genmake2 -mods=../code
460    % make depend
461    % make
462    \end{verbatim}
463    This builds the code exactly as before but this time you need to copy
464    either the executable or the input files or both in order to run the
465    model. For example,
466    \begin{verbatim}
467    % cp ../input/* ./
468    % ./mitgcmuv > output.txt
469    \end{verbatim}
470    or if you tend to make multiple runs with the same executable then
471    running in a new directory each time might be more appropriate:
472    \begin{verbatim}
473    % cd ../
474    % mkdir run1
475    % cp build/mitgcmuv run1/
476    % cp input/* run1/
477    % cd run1
478    % ./mitgcmuv > output.txt
479    \end{verbatim}
480    
481    \subsubsection{Building on a scratch disk}
482    
483    Model object files and output data can use up large amounts of disk
484    space so it is often the case that you will be operating on a large
485    scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
486    following commands will build the model in {\em /scratch/exp2-run1}:
487    \begin{verbatim}
488    % cd /scratch/exp2-run1
489    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
490      -mods=~/MITgcm/verification/exp2/code
491    % make depend
492    % make
493    \end{verbatim}
494    To run the model here, you'll need the input files:
495    \begin{verbatim}
496    % cp ~/MITgcm/verification/exp2/input/* ./
497    % ./mitgcmuv > output.txt
498    \end{verbatim}
499    
500    As before, you could build in one directory and make multiple runs of
501    the one experiment:
502    \begin{verbatim}
503    % cd /scratch/exp2
504    % mkdir build
505    % cd build
506    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
507      -mods=~/MITgcm/verification/exp2/code
508    % make depend
509    % make
510    % cd ../
511    % cp -r ~/MITgcm/verification/exp2/input run2
512    % cd run2
513    % ./mitgcmuv > output.txt
514    \end{verbatim}
515    
516    
517    \subsection{Using \texttt{genmake2}}
518    \label{sect:genmake}
519    
520    To compile the code, first use the program \texttt{genmake2} (located
521    in the \texttt{tools} directory) to generate a Makefile.
522    \texttt{genmake2} is a shell script written to work with all
523    ``sh''--compatible shells including bash v1, bash v2, and Bourne.
524    Internally, \texttt{genmake2} determines the locations of needed
525    files, the compiler, compiler options, libraries, and Unix tools.  It
526    relies upon a number of ``optfiles'' located in the
527    \texttt{tools/build\_options} directory.
528    
529    The purpose of the optfiles is to provide all the compilation options
530    for particular ``platforms'' (where ``platform'' roughly means the
531    combination of the hardware and the compiler) and code configurations.
532    Given the combinations of possible compilers and library dependencies
533    ({\it eg.}  MPI and NetCDF) there may be numerous optfiles available
534    for a single machine.  The naming scheme for the majority of the
535    optfiles shipped with the code is
536    \begin{center}
537      {\bf OS\_HARDWARE\_COMPILER }
538    \end{center}
539    where
540    \begin{description}
541    \item[OS] is the name of the operating system (generally the
542      lower-case output of the {\tt 'uname'} command)
543    \item[HARDWARE] is a string that describes the CPU type and
544      corresponds to output from the  {\tt 'uname -m'} command:
545      \begin{description}
546      \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
547        and athlon
548      \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
549      \item[amd64] is AMD x86\_64 systems
550      \item[ppc] is for Mac PowerPC systems
551      \end{description}
552    \item[COMPILER] is the compiler name (generally, the name of the
553      FORTRAN executable)
554    \end{description}
555    
556    In many cases, the default optfiles are sufficient and will result in
557    usable Makefiles.  However, for some machines or code configurations,
558    new ``optfiles'' must be written. To create a new optfile, it is
559    generally best to start with one of the defaults and modify it to suit
560    your needs.  Like \texttt{genmake2}, the optfiles are all written
561    using a simple ``sh''--compatible syntax.  While nearly all variables
562    used within \texttt{genmake2} may be specified in the optfiles, the
563    critical ones that should be defined are:
564    
565    \begin{description}
566    \item[FC] the FORTRAN compiler (executable) to use
567    \item[DEFINES] the command-line DEFINE options passed to the compiler
568    \item[CPP] the C pre-processor to use
569    \item[NOOPTFLAGS] options flags for special files that should not be
570      optimized
571    \end{description}
572    
573    For example, the optfile for a typical Red Hat Linux machine (``ia32''
574    architecture) using the GCC (g77) compiler is
575    \begin{verbatim}
576    FC=g77
577    DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
578    CPP='cpp  -traditional -P'
579    NOOPTFLAGS='-O0'
580    #  For IEEE, use the "-ffloat-store" option
581    if test "x$IEEE" = x ; then
582        FFLAGS='-Wimplicit -Wunused -Wuninitialized'
583        FOPTIM='-O3 -malign-double -funroll-loops'
584    else
585        FFLAGS='-Wimplicit -Wunused -ffloat-store'
586        FOPTIM='-O0 -malign-double'
587    fi
588    \end{verbatim}
589    
590    If you write an optfile for an unrepresented machine or compiler, you
591    are strongly encouraged to submit the optfile to the MITgcm project
592    for inclusion.  Please send the file to the
593    \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
594    \begin{center}
595      MITgcm-support@mitgcm.org
596    \end{center}
597    \begin{rawhtml} </A> \end{rawhtml}
598    mailing list.
599    
600    In addition to the optfiles, \texttt{genmake2} supports a number of
601    helpful command-line options.  A complete list of these options can be
602    obtained from:
603    \begin{verbatim}
604    % genmake2 -h
605    \end{verbatim}
606    
607    The most important command-line options are:
608    \begin{description}
609      
610    \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
611      should be used for a particular build.
612      
613      If no "optfile" is specified (either through the command line or the
614      MITGCM\_OPTFILE environment variable), genmake2 will try to make a
615      reasonable guess from the list provided in {\em
616        tools/build\_options}.  The method used for making this guess is
617      to first determine the combination of operating system and hardware
618      (eg. "linux\_ia32") and then find a working FORTRAN compiler within
619      the user's path.  When these three items have been identified,
620      genmake2 will try to find an optfile that has a matching name.
621      
622    \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
623      set of packages to be used.  The normal order of precedence for
624      packages is as follows:
625      \begin{enumerate}
626      \item If available, the command line (\texttt{--pdefault}) settings
627        over-rule any others.
628    
629      \item Next, \texttt{genmake2} will look for a file named
630        ``\texttt{packages.conf}'' in the local directory or in any of the
631        directories specified with the \texttt{--mods} option.
632        
633      \item Finally, if neither of the above are available,
634        \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
635      \end{enumerate}
636      
637    \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
638      used for packages.
639      
640      If not specified, the default dependency file {\em pkg/pkg\_depend}
641      is used.  The syntax for this file is parsed on a line-by-line basis
642      where each line containes either a comment ("\#") or a simple
643      "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol
644      specifies a "must be used with" or a "must not be used with"
645      relationship, respectively.  If no rule is specified, then it is
646      assumed that the two packages are compatible and will function
647      either with or without each other.
648      
649    \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
650      automatic differentiation options file to be used.  The file is
651      analogous to the ``optfile'' defined above but it specifies
652      information for the AD build process.
653      
654      The default file is located in {\em
655        tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
656      and "TAMC" compilers.  An alternate version is also available at
657      {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
658      "STAF" compiler.  As with any compilers, it is helpful to have their
659      directories listed in your {\tt \$PATH} environment variable.
660      
661    \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
662      directories containing ``modifications''.  These directories contain
663      files with names that may (or may not) exist in the main MITgcm
664      source tree but will be overridden by any identically-named sources
665      within the ``MODS'' directories.
666      
667      The order of precedence for this "name-hiding" is as follows:
668      \begin{itemize}
669      \item ``MODS'' directories (in the order given)
670      \item Packages either explicitly specified or provided by default
671        (in the order given)
672      \item Packages included due to package dependencies (in the order
673        that that package dependencies are parsed)
674      \item The "standard dirs" (which may have been specified by the
675        ``-standarddirs'' option)
676      \end{itemize}
677      
678    \item[\texttt{--mpi}] This option enables certain MPI features (using
679      CPP \texttt{\#define}s) within the code and is necessary for MPI
680      builds (see Section \ref{sect:mpi-build}).
681      
682    \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
683      soft-links and other bugs common with the \texttt{make} versions
684      provided by commercial Unix vendors, GNU \texttt{make} (sometimes
685      called \texttt{gmake}) should be preferred.  This option provides a
686      means for specifying the make executable to be used.
687      
688    \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
689      machines, the ``bash'' shell is unavailable.  To run on these
690      systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
691      a Bourne, POSIX, or compatible) shell.  The syntax in these
692      circumstances is:
693      \begin{center}
694        \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
695      \end{center}
696      where \texttt{/bin/sh} can be replaced with the full path and name
697      of the desired shell.
698    
699    \end{description}
700    
701    
702    \subsection{Building with MPI}
703    \label{sect:mpi-build}
704    
705    Building MITgcm to use MPI libraries can be complicated due to the
706    variety of different MPI implementations available, their dependencies
707    or interactions with different compilers, and their often ad-hoc
708    locations within file systems.  For these reasons, its generally a
709    good idea to start by finding and reading the documentation for your
710    machine(s) and, if necessary, seeking help from your local systems
711    administrator.
712    
713    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    An example of the above process on the MITgcm cluster (``cg01'') using
784    the GNU g77 compiler and the mpich MPI library is:
785    
786    {\footnotesize \begin{verbatim}
787      %  cd MITgcm/verification/exp5
788      %  mkdir build
789      %  cd build
790      %  ../../../tools/genmake2 -mpi -mods=../code \
791           -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
792      %  make depend
793      %  make
794      %  cd ../input
795      %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
796           -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
797    \end{verbatim} }
798    
799  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
800  \label{sect:runModel}  \label{sect:runModel}
# Line 587  output.txt}. Line 802  output.txt}.
802  <!-- CMIREDIR:runModel: -->  <!-- CMIREDIR:runModel: -->
803  \end{rawhtml}  \end{rawhtml}
804    
805  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sect:buildingCode})
806  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
807  local directory.  local directory.
808    
# Line 602  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}
# Line 610  In the event that the model encounters a Line 825  In the event that the model encounters a
825  helpful to include the last few line of this \texttt{output.txt} file  helpful to include the last few line of this \texttt{output.txt} file
826  along with the (\texttt{stderr}) error message within any bug reports.  along with the (\texttt{stderr}) error message within any bug reports.
827    
828  For the example experiments in {\em verification}, an example of the  For the example experiments in \texttt{verification}, an example of the
829  output is kept in {\em results/output.txt} for comparison. You can  output is kept in \texttt{results/output.txt} for comparison. You can
830  compare your {\em output.txt} with the corresponding one for that  compare your \texttt{output.txt} with the corresponding one for that
831  experiment to check that the set-up works.  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.  Depending upon the I/O  The model produces various output files and, when using \texttt{mnc},
838  package selected (either \texttt{mdsio} or \texttt{mnc} or both as  sometimes even directories.  Depending upon the I/O package(s)
839  determined by both the compile-time settings and the run-time flags in  selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
840  \texttt{data.pkg}), the following output may appear.  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}  \subsubsection{MDSIO output files}
# Line 632  package.  At a minimum, the instantaneou Line 849  package.  At a minimum, the instantaneou
849  written out, which is made of the following files:  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 667  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    
# Line 687  a name such as \texttt{mnc\_test\_\${DAT Line 904  a name such as \texttt{mnc\_test\_\${DAT
904  within this subdirectory are all in the ``self-describing'' netCDF  within this subdirectory are all in the ``self-describing'' netCDF
905  format and can thus be browsed and/or plotted using tools such as:  format and can thus be browsed and/or plotted using tools such as:
906  \begin{itemize}  \begin{itemize}
907  \item At a minimum, the \texttt{ncdump} utility is typically included  \item \texttt{ncdump} is a utility which is typically included
908    with every netCDF install:    with every netCDF install:
909    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
910  \begin{verbatim}  \begin{verbatim}
911  http://www.unidata.ucar.edu/packages/netcdf/  http://www.unidata.ucar.edu/packages/netcdf/
912  \end{verbatim}  \end{verbatim}
913    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
914      binaries into formatted ASCII text files.
915    
916  \item The \texttt{ncview} utility is a very convenient and quick way  \item \texttt{ncview} utility is a very convenient and quick way
917    to plot netCDF data and it runs on most OSes:    to plot netCDF data and it runs on most OSes:
918    \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}    \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
919  \begin{verbatim}  \begin{verbatim}
# Line 705  http://meteora.ucsd.edu/~pierce/ncview_h Line 923  http://meteora.ucsd.edu/~pierce/ncview_h
923        
924  \item MatLAB(c) and other common post-processing environments provide  \item MatLAB(c) and other common post-processing environments provide
925    various netCDF interfaces including:    various netCDF interfaces including:
926      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
927    \begin{verbatim}
928    http://mexcdf.sourceforge.net/
929    \end{verbatim}
930      \begin{rawhtml} </A> \end{rawhtml}
931    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
932  \begin{verbatim}  \begin{verbatim}
933  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
934  \end{verbatim}  \end{verbatim}
935    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
   
936  \end{itemize}  \end{itemize}
937    
938    
# Line 718  http://woodshole.er.usgs.gov/staffpages/ Line 940  http://woodshole.er.usgs.gov/staffpages/
940    
941  The ``traditional'' or mdsio model data are written according to a  The ``traditional'' or mdsio model data are written according to a
942  ``meta/data'' file format.  Each variable is associated with two files  ``meta/data'' file format.  Each variable is associated with two files
943  with suffix names \textit{.data} and \textit{.meta}. The  with suffix names \texttt{.data} and \texttt{.meta}. The
944  \textit{.data} file contains the data written in binary form  \texttt{.data} file contains the data written in binary form
945  (big\_endian by default). The \textit{.meta} file is a ``header'' file  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
946  that contains information about the size and the structure of the  that contains information about the size and the structure of the
947  \textit{.data} file. This way of organizing the output is particularly  \texttt{.data} file. This way of organizing the output is particularly
948  useful when running multi-processors calculations. The base version of  useful when running multi-processors calculations. The base version of
949  the model includes a few matlab utilities to read output files written  the model includes a few matlab utilities to read output files written
950  in this format. The matlab scripts are located in the directory  in this format. The matlab scripts are located in the directory
951  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m}  \texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m}
952  reads the data. Look at the comments inside the script to see how to  reads the data. Look at the comments inside the script to see how to
953  use it.  use it.
954    
# Line 745  Some examples of reading and visualizing Line 967  Some examples of reading and visualizing
967  >> 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
968  \end{verbatim}  \end{verbatim}
969    
970  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available.  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
971    they are described in Section \ref{sec:pkg:mnc}.
972    
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