/[MITgcm]/manual/s_getstarted/text/getting_started.tex
ViewVC logotype

Diff of /manual/s_getstarted/text/getting_started.tex

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.28 by cnh, Thu Oct 14 14:54:24 2004 UTC revision 1.44 by jmc, Mon Aug 30 23:09:20 2010 UTC
# 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{sec: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{sec: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 80  provide easy support for maintenance upd Line 63  provide easy support for maintenance upd
63  \end{enumerate}  \end{enumerate}
64    
65  \subsection{Method 1 - Checkout from CVS}  \subsection{Method 1 - Checkout from CVS}
66  \label{sect:cvs_checkout}  \label{sec:cvs_checkout}
67    
68  If CVS is available on your system, we strongly encourage you to use it. CVS  If CVS is available on your system, we strongly encourage you to use it. CVS
69  provides an efficient and elegant way of organizing your code and keeping  provides an efficient and elegant way of organizing your code and keeping
# 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/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
106  \begin{verbatim}  \begin{verbatim}
107  http://mitgcm.org/source_code.html  http://mitgcm.org/viewvc/MITgcm/MITgcm/
108  \end{verbatim}  \end{verbatim}
109  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
110    
# 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/public/using_cvs.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{sec: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  \item \textit{verification}: this directory contains the model    decompositions.
   examples. See section \ref{sect:modelExamples}.  
   
 \end{itemize}  
   
 \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}.  
     
 \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).  
301        
302  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  \item \texttt{verification}: this directory contains the model
303    physics. 3D Equatorial Channel configuration.    examples. See section \ref{sec:modelExamples}.
     
 \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}.  
304    
305  \item \textit{flt\_example} Example of using float package.  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
306        
307  \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux  \item \texttt{lsopt}: Line search code used for optimization.
   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}.  
308        
309  \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube  \item \texttt{optim}: Interface between MITgcm and line search code.
   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}  
310        
   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{sec: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{sec: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{sec: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}
411    
412    In the example above (section \ref{sec:buildingCode}) we built the
413    executable in the {\em input} directory of the experiment for
414    convenience. You can also configure and compile the code in other
415    locations, for example on a scratch disk with out having to copy the
416    entire source tree. The only requirement to do so is you have {\tt
417      genmake2} in your path or you know the absolute path to {\tt
418      genmake2}.
419    
420    The following sections outline some possible methods of organizing
421    your source and data.
422    
423    \subsubsection{Building from the {\em ../code directory}}
424    
425    This is just as simple as building in the {\em input/} directory:
426    \begin{verbatim}
427    % cd verification/exp2/code
428    % ../../../tools/genmake2
429    % make depend
430    % make
431    \end{verbatim}
432    However, to run the model the executable ({\em mitgcmuv}) and input
433    files must be in the same place. If you only have one calculation to make:
434    \begin{verbatim}
435    % cd ../input
436    % cp ../code/mitgcmuv ./
437    % ./mitgcmuv > output.txt
438    \end{verbatim}
439    or if you will be making multiple runs with the same executable:
440    \begin{verbatim}
441    % cd ../
442    % cp -r input run1
443    % cp code/mitgcmuv run1
444    % cd run1
445    % ./mitgcmuv > output.txt
446    \end{verbatim}
447    
448    \subsubsection{Building from a new directory}
449    
450    Since the {\em input} directory contains input files it is often more
451    useful to keep {\em input} pristine and build in a new directory
452    within {\em verification/exp2/}:
453    \begin{verbatim}
454    % cd verification/exp2
455    % mkdir build
456    % cd build
457    % ../../../tools/genmake2 -mods=../code
458    % make depend
459    % make
460    \end{verbatim}
461    This builds the code exactly as before but this time you need to copy
462    either the executable or the input files or both in order to run the
463    model. For example,
464    \begin{verbatim}
465    % cp ../input/* ./
466    % ./mitgcmuv > output.txt
467    \end{verbatim}
468    or if you tend to make multiple runs with the same executable then
469    running in a new directory each time might be more appropriate:
470    \begin{verbatim}
471    % cd ../
472    % mkdir run1
473    % cp build/mitgcmuv run1/
474    % cp input/* run1/
475    % cd run1
476    % ./mitgcmuv > output.txt
477    \end{verbatim}
478    
479    \subsubsection{Building on a scratch disk}
480    
481    Model object files and output data can use up large amounts of disk
482    space so it is often the case that you will be operating on a large
483    scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
484    following commands will build the model in {\em /scratch/exp2-run1}:
485    \begin{verbatim}
486    % cd /scratch/exp2-run1
487    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
488      -mods=~/MITgcm/verification/exp2/code
489    % make depend
490    % make
491    \end{verbatim}
492    To run the model here, you'll need the input files:
493    \begin{verbatim}
494    % cp ~/MITgcm/verification/exp2/input/* ./
495    % ./mitgcmuv > output.txt
496    \end{verbatim}
497    
498    As before, you could build in one directory and make multiple runs of
499    the one experiment:
500    \begin{verbatim}
501    % cd /scratch/exp2
502    % mkdir build
503    % cd build
504    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
505      -mods=~/MITgcm/verification/exp2/code
506    % make depend
507    % make
508    % cd ../
509    % cp -r ~/MITgcm/verification/exp2/input run2
510    % cd run2
511    % ./mitgcmuv > output.txt
512    \end{verbatim}
513    
514    
515    \subsection{Using \texttt{genmake2}}
516    \label{sec:genmake}
517    
518    To compile the code, first use the program \texttt{genmake2} (located
519    in the \texttt{tools} directory) to generate a Makefile.
520    \texttt{genmake2} is a shell script written to work with all
521    ``sh''--compatible shells including bash v1, bash v2, and Bourne.
522    %Internally, \texttt{genmake2} determines the locations of needed
523    %files, the compiler, compiler options, libraries, and Unix tools.  It
524    %relies upon a number of ``optfiles'' located in the
525    %\texttt{tools/build\_options} directory.
526    \texttt{genmake2} parses information from the following sources:
527    \begin{description}
528    \item[-] a {\em gemake\_local} file if one is found in the current
529      directory
530    \item[-] command-line options
531    \item[-] an "options file" as specified by the command-line option
532      \texttt{--optfile=/PATH/FILENAME}
533    \item[-] a {\em packages.conf} file (if one is found) with the
534      specific list of packages to compile. The search path for
535      file {\em packages.conf} is, first, the current directory and
536      then each of the "MODS" directories in the given order (see below).
537    \end{description}
538    
539    \subsubsection{Optfiles in \texttt{tools/build\_options} directory:}
540    
541    The purpose of the optfiles is to provide all the compilation options
542    for particular ``platforms'' (where ``platform'' roughly means the
543    combination of the hardware and the compiler) and code configurations.
544    Given the combinations of possible compilers and library dependencies
545    ({\it eg.}  MPI and NetCDF) there may be numerous optfiles available
546    for a single machine.  The naming scheme for the majority of the
547    optfiles shipped with the code is
548    \begin{center}
549      {\bf OS\_HARDWARE\_COMPILER }
550    \end{center}
551    where
552    \begin{description}
553    \item[OS] is the name of the operating system (generally the
554      lower-case output of the {\tt 'uname'} command)
555    \item[HARDWARE] is a string that describes the CPU type and
556      corresponds to output from the  {\tt 'uname -m'} command:
557      \begin{description}
558      \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
559        and athlon
560      \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
561      \item[amd64] is AMD x86\_64 systems
562      \item[ppc] is for Mac PowerPC systems
563      \end{description}
564    \item[COMPILER] is the compiler name (generally, the name of the
565      FORTRAN executable)
566    \end{description}
567    
568    In many cases, the default optfiles are sufficient and will result in
569    usable Makefiles.  However, for some machines or code configurations,
570    new ``optfiles'' must be written. To create a new optfile, it is
571    generally best to start with one of the defaults and modify it to suit
572    your needs.  Like \texttt{genmake2}, the optfiles are all written
573    using a simple ``sh''--compatible syntax.  While nearly all variables
574    used within \texttt{genmake2} may be specified in the optfiles, the
575    critical ones that should be defined are:
576    
577    \begin{description}
578    \item[FC] the FORTRAN compiler (executable) to use
579    \item[DEFINES] the command-line DEFINE options passed to the compiler
580    \item[CPP] the C pre-processor to use
581    \item[NOOPTFLAGS] options flags for special files that should not be
582      optimized
583    \end{description}
584    
585    For example, the optfile for a typical Red Hat Linux machine (``ia32''
586    architecture) using the GCC (g77) compiler is
587    \begin{verbatim}
588    FC=g77
589    DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
590    CPP='cpp  -traditional -P'
591    NOOPTFLAGS='-O0'
592    #  For IEEE, use the "-ffloat-store" option
593    if test "x$IEEE" = x ; then
594        FFLAGS='-Wimplicit -Wunused -Wuninitialized'
595        FOPTIM='-O3 -malign-double -funroll-loops'
596    else
597        FFLAGS='-Wimplicit -Wunused -ffloat-store'
598        FOPTIM='-O0 -malign-double'
599    fi
600    \end{verbatim}
601    
602    If you write an optfile for an unrepresented machine or compiler, you
603    are strongly encouraged to submit the optfile to the MITgcm project
604    for inclusion.  Please send the file to the
605    \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
606    \begin{center}
607      MITgcm-support@mitgcm.org
608    \end{center}
609    \begin{rawhtml} </A> \end{rawhtml}
610    mailing list.
611    
612    \subsubsection{Command-line options:}
613    
614    In addition to the optfiles, \texttt{genmake2} supports a number of
615    helpful command-line options.  A complete list of these options can be
616    obtained from:
617    \begin{verbatim}
618    % genmake2 -h
619    \end{verbatim}
620    
621    The most important command-line options are:
622    \begin{description}
623      
624    \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
625      should be used for a particular build.
626      
627      If no "optfile" is specified (either through the command line or the
628      MITGCM\_OPTFILE environment variable), genmake2 will try to make a
629      reasonable guess from the list provided in {\em
630        tools/build\_options}.  The method used for making this guess is
631      to first determine the combination of operating system and hardware
632      (eg. "linux\_ia32") and then find a working FORTRAN compiler within
633      the user's path.  When these three items have been identified,
634      genmake2 will try to find an optfile that has a matching name.
635      
636    \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
637      directories containing ``modifications''.  These directories contain
638      files with names that may (or may not) exist in the main MITgcm
639      source tree but will be overridden by any identically-named sources
640      within the ``MODS'' directories.
641      
642      The order of precedence for this "name-hiding" is as follows:
643      \begin{itemize}
644      \item ``MODS'' directories (in the order given)
645      \item Packages either explicitly specified or provided by default
646        (in the order given)
647      \item Packages included due to package dependencies (in the order
648        that that package dependencies are parsed)
649      \item The "standard dirs" (which may have been specified by the
650        ``-standarddirs'' option)
651      \end{itemize}
652      
653    \item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
654      where package groups are defined. If not set, the package-groups
655      definition will be read from {\em pkg/pkg\_groups}.
656      It also contains the default list of packages (defined
657      as the group ``{\it default\_pkg\_list}'' which is used
658      when no specific package list ({\em packages.conf})
659      is found in current directory or in any "MODS" directory.
660    
661    \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
662      used for packages.
663      
664      If not specified, the default dependency file {\em pkg/pkg\_depend}
665      is used.  The syntax for this file is parsed on a line-by-line basis
666      where each line containes either a comment ("\#") or a simple
667      "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol
668      specifies a "must be used with" or a "must not be used with"
669      relationship, respectively.  If no rule is specified, then it is
670      assumed that the two packages are compatible and will function
671      either with or without each other.
672      
673    \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
674      automatic differentiation options file to be used.  The file is
675      analogous to the ``optfile'' defined above but it specifies
676      information for the AD build process.
677      
678      The default file is located in {\em
679        tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
680      and "TAMC" compilers.  An alternate version is also available at
681      {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
682      "STAF" compiler.  As with any compilers, it is helpful to have their
683      directories listed in your {\tt \$PATH} environment variable.
684      
685    \item[\texttt{--mpi}] This option enables certain MPI features (using
686      CPP \texttt{\#define}s) within the code and is necessary for MPI
687      builds (see Section \ref{sec:mpi-build}).
688      
689    \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
690      soft-links and other bugs common with the \texttt{make} versions
691      provided by commercial Unix vendors, GNU \texttt{make} (sometimes
692      called \texttt{gmake}) should be preferred.  This option provides a
693      means for specifying the make executable to be used.
694      
695    \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
696      machines, the ``bash'' shell is unavailable.  To run on these
697      systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
698      a Bourne, POSIX, or compatible) shell.  The syntax in these
699      circumstances is:
700      \begin{center}
701        \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
702      \end{center}
703      where \texttt{/bin/sh} can be replaced with the full path and name
704      of the desired shell.
705    
706    \end{description}
707    
708    
709    \subsection{Building with MPI}
710    \label{sec:mpi-build}
711    
712    Building MITgcm to use MPI libraries can be complicated due to the
713    variety of different MPI implementations available, their dependencies
714    or interactions with different compilers, and their often ad-hoc
715    locations within file systems.  For these reasons, its generally a
716    good idea to start by finding and reading the documentation for your
717    machine(s) and, if necessary, seeking help from your local systems
718    administrator.
719    
720    The steps for building MITgcm with MPI support are:
721    \begin{enumerate}
722      
723    \item Determine the locations of your MPI-enabled compiler and/or MPI
724      libraries and put them into an options file as described in Section
725      \ref{sec:genmake}.  One can start with one of the examples in:
726      \begin{rawhtml} <A
727        href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
728      \end{rawhtml}
729      \begin{center}
730        \texttt{MITgcm/tools/build\_options/}
731      \end{center}
732      \begin{rawhtml} </A> \end{rawhtml}
733      such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
734      \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
735      hand.  You may need help from your user guide or local systems
736      administrator to determine the exact location of the MPI libraries.
737      If libraries are not installed, MPI implementations and related
738      tools are available including:
739      \begin{itemize}
740      \item \begin{rawhtml} <A
741          href="http://www-unix.mcs.anl.gov/mpi/mpich/">
742        \end{rawhtml}
743        MPICH
744        \begin{rawhtml} </A> \end{rawhtml}
745    
746      \item \begin{rawhtml} <A
747          href="http://www.lam-mpi.org/">
748        \end{rawhtml}
749        LAM/MPI
750        \begin{rawhtml} </A> \end{rawhtml}
751    
752      \item \begin{rawhtml} <A
753          href="http://www.osc.edu/~pw/mpiexec/">
754        \end{rawhtml}
755        MPIexec
756        \begin{rawhtml} </A> \end{rawhtml}
757      \end{itemize}
758      
759    \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
760      (see Section \ref{sec:genmake}) using commands such as:
761    {\footnotesize \begin{verbatim}
762      %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
763      %  make depend
764      %  make
765    \end{verbatim} }
766      
767    \item Run the code with the appropriate MPI ``run'' or ``exec''
768      program provided with your particular implementation of MPI.
769      Typical MPI packages such as MPICH will use something like:
770    \begin{verbatim}
771      %  mpirun -np 4 -machinefile mf ./mitgcmuv
772    \end{verbatim}
773      Sightly more complicated scripts may be needed for many machines
774      since execution of the code may be controlled by both the MPI
775      library and a job scheduling and queueing system such as PBS,
776      LoadLeveller, Condor, or any of a number of similar tools.  A few
777      example scripts (those used for our \begin{rawhtml} <A
778        href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
779      verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
780      at:
781      \begin{rawhtml} <A
782        href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/">
783      \end{rawhtml}
784      {\footnotesize \tt
785        http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
786      \begin{rawhtml} </A> \end{rawhtml}
787      or at:
788      \begin{rawhtml} <A
789        href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
790      \end{rawhtml}
791      {\footnotesize \tt
792        http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
793      \begin{rawhtml} </A> \end{rawhtml}
794    
795    \end{enumerate}
796    
797    An example of the above process on the MITgcm cluster (``cg01'') using
798    the GNU g77 compiler and the mpich MPI library is:
799    
800    {\footnotesize \begin{verbatim}
801      %  cd MITgcm/verification/exp5
802      %  mkdir build
803      %  cd build
804      %  ../../../tools/genmake2 -mpi -mods=../code \
805           -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
806      %  make depend
807      %  make
808      %  cd ../input
809      %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
810           -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
811    \end{verbatim} }
812    
813  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
814  \label{sect:runModel}  \label{sec:runModel}
815    \begin{rawhtml}
816    <!-- CMIREDIR:runModel: -->
817    \end{rawhtml}
818    
819  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sec:buildingCode})
820  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
821  local directory.  local directory.
822    
823  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)
824  type:  simply type:
825  \begin{verbatim}  \begin{verbatim}
826  % ./mitgcmuv  % ./mitgcmuv
827  \end{verbatim}  \end{verbatim}
# Line 579  do!). The above command will spew out ma Line 831  do!). The above command will spew out ma
831  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
832  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
833  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
834  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
835  \begin{verbatim}  \begin{verbatim}
836  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
837  \end{verbatim}  \end{verbatim}
838    In the event that the model encounters an error and stops, it is very
839  For the example experiments in {\em verification}, an example of the  helpful to include the last few line of this \texttt{output.txt} file
840  output is kept in {\em results/output.txt} for comparison. You can compare  along with the (\texttt{stderr}) error message within any bug reports.
841  your {\em output.txt} with this one to check that the set-up works.  
842    For the example experiments in \texttt{verification}, an example of the
843    output is kept in \texttt{results/output.txt} for comparison. You can
844    compare your \texttt{output.txt} with the corresponding one for that
845    experiment to check that the set-up works.
846    
847    
848    
849  \subsection{Output files}  \subsection{Output files}
850    
851  The model produces various output files. At a minimum, the instantaneous  The model produces various output files and, when using \texttt{mnc},
852  ``state'' of the model is written out, which is made of the following files:  sometimes even directories.  Depending upon the I/O package(s)
853    selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
854    both as determined by \texttt{code/packages.conf}) and the run-time
855    flags set (in \texttt{input/data.pkg}), the following output may
856    appear.
857    
858    
859    \subsubsection{MDSIO output files}
860    
861    The ``traditional'' output files are generated by the \texttt{mdsio}
862    package.  At a minimum, the instantaneous ``state'' of the model is
863    written out, which is made of the following files:
864    
865  \begin{itemize}  \begin{itemize}
866  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
867  0 $ eastward).    and positive eastward).
868    
869  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
870  and $> 0$ northward).    (m/s and positive northward).
871    
872  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
873  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
874  i.e. downward).    towards increasing pressure i.e. downward).
875    
876  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
877  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
878    
879  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
880  (g/kg).    vapor (g/kg).
881    
882  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
883  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
884  \end{itemize}  \end{itemize}
885    
886  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
887  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
888  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
889    
890  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
891    
892  \begin{itemize}  \begin{itemize}
893  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
894  \end{itemize}  \end{itemize}
895    
896  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 631  form and is used for restarting the inte Line 898  form and is used for restarting the inte
898  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
899    
900  \begin{itemize}  \begin{itemize}
901  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
902  \end{itemize}  \end{itemize}
903    
904  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
905  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
906  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
907  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
908  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
909  output to save disk space during long integrations.  output to save disk space during long integrations.
910    
911    \subsubsection{MNC output files}
912    
913    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
914    is usually (though not necessarily) placed within a subdirectory with
915    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  
916    
917  \subsection{Looking at the output}  \subsection{Looking at the output}
918    
919  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
920  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
921  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \texttt{.data} and \texttt{.meta}. The
922  binary form (big\_endian by default). The \textit{.meta} file is a  \texttt{.data} file contains the data written in binary form
923  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
924  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
925  particularly useful when running multi-processors calculations. The base  \texttt{.data} file. This way of organizing the output is particularly
926  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
927  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
928  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
929  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}
930    reads the data. Look at the comments inside the script to see how to
931    use it.
932    
933  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
934  \begin{verbatim}  \begin{verbatim}
# Line 670  Some examples of reading and visualizing Line 945  Some examples of reading and visualizing
945  >> 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
946  \end{verbatim}  \end{verbatim}
947    
948    Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
949    they are described in Section \ref{sec:pkg:mnc}.
950    
951    The MNC output files are all in the ``self-describing'' netCDF
952    format and can thus be browsed and/or plotted using tools such as:
953    \begin{itemize}
954    \item \texttt{ncdump} is a utility which is typically included
955      with every netCDF install:
956      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
957    \begin{verbatim}
958    http://www.unidata.ucar.edu/packages/netcdf/
959    \end{verbatim}
960      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
961      binaries into formatted ASCII text files.
962    
963    \item \texttt{ncview} utility is a very convenient and quick way
964      to plot netCDF data and it runs on most OSes:
965      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
966    \begin{verbatim}
967    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
968    \end{verbatim}
969      \begin{rawhtml} </A> \end{rawhtml}
970      
971    \item MatLAB(c) and other common post-processing environments provide
972      various netCDF interfaces including:
973      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
974    \begin{verbatim}
975    http://mexcdf.sourceforge.net/
976    \end{verbatim}
977      \begin{rawhtml} </A> \end{rawhtml}
978      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
979    \begin{verbatim}
980    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
981    \end{verbatim}
982      \begin{rawhtml} </A> \end{rawhtml}
983    \end{itemize}
984    
Legend:
Removed from v.1.28  
changed lines
  Added in v.1.44
  ViewVC Help
Powered by ViewVC 1.1.22