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revision 1.37 by molod, Wed Jun 28 16:48:19 2006 UTC revision 1.46 by dimitri, Sat Nov 21 03:19:54 2015 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}  \begin{rawhtml}
19  <!-- CMIREDIR:whereToFindInfo: -->  <!-- CMIREDIR:whereToFindInfo: -->
20  \end{rawhtml}  \end{rawhtml}
# Line 31  http://mitgcm.org/pipermail/mitgcm-suppo Line 29  http://mitgcm.org/pipermail/mitgcm-suppo
29  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
30    
31  \section{Obtaining the code}  \section{Obtaining the code}
32  \label{sect:obtainingCode}  \label{sec:obtainingCode}
33  \begin{rawhtml}  \begin{rawhtml}
34  <!-- CMIREDIR:obtainingCode: -->  <!-- CMIREDIR:obtainingCode: -->
35  \end{rawhtml}  \end{rawhtml}
# Line 65  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 94  You only need to do a ``cvs login'' once Line 92  You only need to do a ``cvs login'' once
92    
93  To obtain the latest sources type:  To obtain the latest sources type:
94  \begin{verbatim}  \begin{verbatim}
95  % cvs co MITgcm  % cvs co -P MITgcm
96  \end{verbatim}  \end{verbatim}
97  or to get a specific release type:  or to get a specific release type:
98  \begin{verbatim}  \begin{verbatim}
99  % cvs co -P -r checkpoint52i_post  MITgcm  % cvs co -P -r checkpoint52i_post MITgcm
100  \end{verbatim}  \end{verbatim}
101    The CVS command ``\texttt{cvs co}'' is the abreviation of the full-name
102    ``\texttt{cvs checkout}'' command and using the option ``-P'' (\texttt{cvs co -P})
103    will prevent to download unnecessary empty directories.
104    
105  The MITgcm web site contains further directions concerning the source  The MITgcm web site contains further directions concerning the source
106  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
107  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
108  development milestones:  development milestones:
109  \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}
110  \begin{verbatim}  \begin{verbatim}
111  http://mitgcm.org/source_code.html  http://mitgcm.org/viewvc/MITgcm/MITgcm/
112  \end{verbatim}  \end{verbatim}
113  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
114    
# Line 141  track of your file versions with respect Line 143  track of your file versions with respect
143  the files in \texttt{CVS}!  You can also use CVS to download code  the files in \texttt{CVS}!  You can also use CVS to download code
144  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
145  MITgcm code can be found  MITgcm code can be found
146  \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}
147  here  here
148  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}.
 .  
149  It is important to note that the CVS aliases in Table  It is important to note that the CVS aliases in Table
150  \ref{tab:cvsModules} cannot be used in conjunction with the CVS  \ref{tab:cvsModules} cannot be used in conjunction with the CVS
151  \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories  \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
152  they create can be changed to a different name following the check-out:  they create can be changed to a different name following the check-out:
153  \begin{verbatim}  \begin{verbatim}
154     %  cvs co MITgcm_verif_basic     %  cvs co -P MITgcm_verif_basic
155     %  mv MITgcm MITgcm_verif_basic     %  mv MITgcm MITgcm_verif_basic
156  \end{verbatim}  \end{verbatim}
157    
158    Note that it is possible to checkout code without ``cvs login'' and without
159    setting any shell environment variables by specifying the pserver name and
160    password in one line, for example:
161    \begin{verbatim}
162       %  cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -P MITgcm
163    \end{verbatim}
164    
165  \subsubsection{Upgrading from an earlier version}  \subsubsection{Upgrading from an earlier version}
166    
167  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 164  your copy instead of downloading the ent Line 172  your copy instead of downloading the ent
172  \end{verbatim}  \end{verbatim}
173  and then issue the cvs update command such as:  and then issue the cvs update command such as:
174  \begin{verbatim}  \begin{verbatim}
175  % cvs -q update -r checkpoint52i_post -d -P  % cvs -q update -d -P -r checkpoint52i_post
176  \end{verbatim}  \end{verbatim}
177  This will update the ``tag'' to ``checkpoint52i\_post'', add any new  This will update the ``tag'' to ``checkpoint52i\_post'', add any new
178  directories (-d) and remove any empty directories (-P). The -q option  directories (-d) and remove any empty directories (-P). The -q option
# Line 210  have run into a problem for which ``we h Line 218  have run into a problem for which ``we h
218  latest code'' and we haven't made a ``tag'' or ``release'' since that  latest code'' and we haven't made a ``tag'' or ``release'' since that
219  patch then you'll need to get the latest code:  patch then you'll need to get the latest code:
220  \begin{verbatim}  \begin{verbatim}
221  % cvs -q update -A -d -P  % cvs -q update -d -P -A
222  \end{verbatim}  \end{verbatim}
223  Unlike, the ``check-out'' and ``update'' procedures above, there is no  Unlike, the ``check-out'' and ``update'' procedures above, there is no
224  ``tag'' or release name. The -A tells CVS to upgrade to the  ``tag'' or release name. The -A tells CVS to upgrade to the
# Line 221  also means we can't tell what version of Line 229  also means we can't tell what version of
229  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
230    
231  \subsection{Method 2 - Tar file download}  \subsection{Method 2 - Tar file download}
232  \label{sect:conventionalDownload}  \label{sec:conventionalDownload}
233    
234  If you do not have CVS on your system, you can download the model as a  If you do not have CVS on your system, you can download the model as a
235  tar file from the web site at:  tar file from the web site at:
236  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/download/ target="idontexist"> \end{rawhtml}
237  \begin{verbatim}  \begin{verbatim}
238  http://mitgcm.org/download/  http://mitgcm.org/download/
239  \end{verbatim}  \end{verbatim}
# Line 278  structure). Line 286  structure).
286    package corresponds to a subdirectory. For example, \texttt{gmredi}    package corresponds to a subdirectory. For example, \texttt{gmredi}
287    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
288    \texttt{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
289    physics. The packages are described in detail in chapter \ref{chap.packagesI}.    physics. The packages are described in detail in chapter \ref{chap:packagesI}.
290        
291  \item \texttt{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
292    For example, \texttt{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
# Line 302  structure). Line 310  structure).
310    decompositions.    decompositions.
311        
312  \item \texttt{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
313    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sec:modelExamples}.
314    
315  \item \texttt{jobs}: contains sample job scripts for running MITgcm.  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
316        
# Line 313  structure). Line 321  structure).
321  \end{itemize}  \end{itemize}
322    
323  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
324  \label{sect:buildingCode}  \label{sec:buildingCode}
325  \begin{rawhtml}  \begin{rawhtml}
326  <!-- CMIREDIR:buildingCode: -->  <!-- CMIREDIR:buildingCode: -->
327  \end{rawhtml}  \end{rawhtml}
# Line 322  To compile the code, we use the \texttt{ Line 330  To compile the code, we use the \texttt{
330  file (\texttt{Makefile}) that allows us to pre-process source files,  file (\texttt{Makefile}) that allows us to pre-process source files,
331  specify compiler and optimization options and also figures out any  specify compiler and optimization options and also figures out any
332  file dependencies. We supply a script (\texttt{genmake2}), described  file dependencies. We supply a script (\texttt{genmake2}), described
333  in section \ref{sect:genmake}, that automatically creates the  in section \ref{sec:genmake}, that automatically creates the
334  \texttt{Makefile} for you. You then need to build the dependencies and  \texttt{Makefile} for you. You then need to build the dependencies and
335  compile the code.  compile the code.
336    
# Line 397  where the ``2'' can be replaced with a n Line 405  where the ``2'' can be replaced with a n
405  number of CPUs available.  number of CPUs available.
406    
407  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
408  given in section \ref{sect:runModel}. Here, we can run the model by  given in section \ref{sec:runModel}. Here, we can run the model by
409  first creating links to all the input files:  first creating links to all the input files:
410  \begin{verbatim}  \begin{verbatim}
411  ln -s ../input/* .  ln -s ../input/* .
# Line 411  where we are re-directing the stream of Line 419  where we are re-directing the stream of
419    
420  \subsection{Building/compiling the code elsewhere}  \subsection{Building/compiling the code elsewhere}
421    
422  In the example above (section \ref{sect:buildingCode}) we built the  In the example above (section \ref{sec:buildingCode}) we built the
423  executable in the {\em input} directory of the experiment for  executable in the {\em input} directory of the experiment for
424  convenience. You can also configure and compile the code in other  convenience. You can also configure and compile the code in other
425  locations, for example on a scratch disk with out having to copy the  locations, for example on a scratch disk with out having to copy the
# Line 515  the one experiment: Line 523  the one experiment:
523    
524    
525  \subsection{Using \texttt{genmake2}}  \subsection{Using \texttt{genmake2}}
526  \label{sect:genmake}  \label{sec:genmake}
527    
528  To compile the code, first use the program \texttt{genmake2} (located  To compile the code, first use the program \texttt{genmake2} (located
529  in the \texttt{tools} directory) to generate a Makefile.  in the \texttt{tools} directory) to generate a Makefile.
530  \texttt{genmake2} is a shell script written to work with all  \texttt{genmake2} is a shell script written to work with all
531  ``sh''--compatible shells including bash v1, bash v2, and Bourne.  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
532  Internally, \texttt{genmake2} determines the locations of needed  %Internally, \texttt{genmake2} determines the locations of needed
533  files, the compiler, compiler options, libraries, and Unix tools.  It  %files, the compiler, compiler options, libraries, and Unix tools.  It
534  relies upon a number of ``optfiles'' located in the  %relies upon a number of ``optfiles'' located in the
535  \texttt{tools/build\_options} directory.  %\texttt{tools/build\_options} directory.
536    \texttt{genmake2} parses information from the following sources:
537    \begin{description}
538    \item[-] a {\em gemake\_local} file if one is found in the current
539      directory
540    \item[-] command-line options
541    \item[-] an "options file" as specified by the command-line option
542      \texttt{--optfile=/PATH/FILENAME}
543    \item[-] a {\em packages.conf} file (if one is found) with the
544      specific list of packages to compile. The search path for
545      file {\em packages.conf} is, first, the current directory and
546      then each of the "MODS" directories in the given order (see below).
547    \end{description}
548    
549    \subsubsection{Optfiles in \texttt{tools/build\_options} directory:}
550    
551  The purpose of the optfiles is to provide all the compilation options  The purpose of the optfiles is to provide all the compilation options
552  for particular ``platforms'' (where ``platform'' roughly means the  for particular ``platforms'' (where ``platform'' roughly means the
# Line 597  for inclusion.  Please send the file to Line 619  for inclusion.  Please send the file to
619  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
620  mailing list.  mailing list.
621    
622    \subsubsection{Command-line options:}
623    
624  In addition to the optfiles, \texttt{genmake2} supports a number of  In addition to the optfiles, \texttt{genmake2} supports a number of
625  helpful command-line options.  A complete list of these options can be  helpful command-line options.  A complete list of these options can be
626  obtained from:  obtained from:
# Line 619  The most important command-line options Line 643  The most important command-line options
643    the user's path.  When these three items have been identified,    the user's path.  When these three items have been identified,
644    genmake2 will try to find an optfile that has a matching name.    genmake2 will try to find an optfile that has a matching name.
645        
646  \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default  \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
647    set of packages to be used.  The normal order of precedence for    directories containing ``modifications''.  These directories contain
648    packages is as follows:    files with names that may (or may not) exist in the main MITgcm
649    \begin{enumerate}    source tree but will be overridden by any identically-named sources
650    \item If available, the command line (\texttt{--pdefault}) settings    within the ``MODS'' directories.
     over-rule any others.  
   
   \item Next, \texttt{genmake2} will look for a file named  
     ``\texttt{packages.conf}'' in the local directory or in any of the  
     directories specified with the \texttt{--mods} option.  
       
   \item Finally, if neither of the above are available,  
     \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.  
   \end{enumerate}  
651        
652      The order of precedence for this "name-hiding" is as follows:
653      \begin{itemize}
654      \item ``MODS'' directories (in the order given)
655      \item Packages either explicitly specified or provided by default
656        (in the order given)
657      \item Packages included due to package dependencies (in the order
658        that that package dependencies are parsed)
659      \item The "standard dirs" (which may have been specified by the
660        ``-standarddirs'' option)
661      \end{itemize}
662      
663    \item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
664      where package groups are defined. If not set, the package-groups
665      definition will be read from {\em pkg/pkg\_groups}.
666      It also contains the default list of packages (defined
667      as the group ``{\it default\_pkg\_list}'' which is used
668      when no specific package list ({\em packages.conf})
669      is found in current directory or in any "MODS" directory.
670    
671  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
672    used for packages.    used for packages.
673        
# Line 658  The most important command-line options Line 692  The most important command-line options
692    "STAF" compiler.  As with any compilers, it is helpful to have their    "STAF" compiler.  As with any compilers, it is helpful to have their
693    directories listed in your {\tt \$PATH} environment variable.    directories listed in your {\tt \$PATH} environment variable.
694        
 \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of  
   directories containing ``modifications''.  These directories contain  
   files with names that may (or may not) exist in the main MITgcm  
   source tree but will be overridden by any identically-named sources  
   within the ``MODS'' directories.  
     
   The order of precedence for this "name-hiding" is as follows:  
   \begin{itemize}  
   \item ``MODS'' directories (in the order given)  
   \item Packages either explicitly specified or provided by default  
     (in the order given)  
   \item Packages included due to package dependencies (in the order  
     that that package dependencies are parsed)  
   \item The "standard dirs" (which may have been specified by the  
     ``-standarddirs'' option)  
   \end{itemize}  
     
695  \item[\texttt{--mpi}] This option enables certain MPI features (using  \item[\texttt{--mpi}] This option enables certain MPI features (using
696    CPP \texttt{\#define}s) within the code and is necessary for MPI    CPP \texttt{\#define}s) within the code and is necessary for MPI
697    builds (see Section \ref{sect:mpi-build}).    builds (see Section \ref{sec:mpi-build}).
698        
699  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
700    soft-links and other bugs common with the \texttt{make} versions    soft-links and other bugs common with the \texttt{make} versions
# Line 700  The most important command-line options Line 717  The most important command-line options
717    
718    
719  \subsection{Building with MPI}  \subsection{Building with MPI}
720  \label{sect:mpi-build}  \label{sec:mpi-build}
721    
722  Building MITgcm to use MPI libraries can be complicated due to the  Building MITgcm to use MPI libraries can be complicated due to the
723  variety of different MPI implementations available, their dependencies  variety of different MPI implementations available, their dependencies
# Line 715  The steps for building MITgcm with MPI s Line 732  The steps for building MITgcm with MPI s
732        
733  \item Determine the locations of your MPI-enabled compiler and/or MPI  \item Determine the locations of your MPI-enabled compiler and/or MPI
734    libraries and put them into an options file as described in Section    libraries and put them into an options file as described in Section
735    \ref{sect:genmake}.  One can start with one of the examples in:    \ref{sec:genmake}.  One can start with one of the examples in:
736    \begin{rawhtml} <A    \begin{rawhtml} <A
737      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
738    \end{rawhtml}    \end{rawhtml}
739    \begin{center}    \begin{center}
740      \texttt{MITgcm/tools/build\_options/}      \texttt{MITgcm/tools/build\_options/}
# Line 750  The steps for building MITgcm with MPI s Line 767  The steps for building MITgcm with MPI s
767    \end{itemize}    \end{itemize}
768        
769  \item Build the code with the \texttt{genmake2} \texttt{-mpi} option  \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
770    (see Section \ref{sect:genmake}) using commands such as:    (see Section \ref{sec:genmake}) using commands such as:
771  {\footnotesize \begin{verbatim}  {\footnotesize \begin{verbatim}
772    %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE    %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
773    %  make depend    %  make depend
# Line 768  The steps for building MITgcm with MPI s Line 785  The steps for building MITgcm with MPI s
785    library and a job scheduling and queueing system such as PBS,    library and a job scheduling and queueing system such as PBS,
786    LoadLeveller, Condor, or any of a number of similar tools.  A few    LoadLeveller, Condor, or any of a number of similar tools.  A few
787    example scripts (those used for our \begin{rawhtml} <A    example scripts (those used for our \begin{rawhtml} <A
788      href="http://mitgcm.org/testing.html"> \end{rawhtml}regular      href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
789    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
790    at:    at:
791    \begin{rawhtml} <A    \begin{rawhtml} <A
792      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/">
793    \end{rawhtml}    \end{rawhtml}
794    {\footnotesize \tt    {\footnotesize \tt
795      http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }      http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
796      \begin{rawhtml} </A> \end{rawhtml}
797      or at:
798      \begin{rawhtml} <A
799        href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
800      \end{rawhtml}
801      {\footnotesize \tt
802        http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
803    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
804    
805  \end{enumerate}  \end{enumerate}
# Line 797  the GNU g77 compiler and the mpich MPI l Line 821  the GNU g77 compiler and the mpich MPI l
821  \end{verbatim} }  \end{verbatim} }
822    
823  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
824  \label{sect:runModel}  \label{sec:runModel}
825  \begin{rawhtml}  \begin{rawhtml}
826  <!-- CMIREDIR:runModel: -->  <!-- CMIREDIR:runModel: -->
827  \end{rawhtml}  \end{rawhtml}
828    
829  If compilation finished succesfully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sec:buildingCode})
830  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
831  local directory.  local directory.
832    
# Line 894  as the pickup files but are named differ Line 918  as the pickup files but are named differ
918  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
919  output to save disk space during long integrations.  output to save disk space during long integrations.
920    
   
   
921  \subsubsection{MNC output files}  \subsubsection{MNC output files}
922    
923  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
924  is usually (though not necessarily) placed within a subdirectory with  is usually (though not necessarily) placed within a subdirectory with
925  a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files  a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  
 within this subdirectory are all in the ``self-describing'' netCDF  
 format and can thus be browsed and/or plotted using tools such as:  
 \begin{itemize}  
 \item \texttt{ncdump} is a utility which is typically included  
   with every netCDF install:  
   \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}  
 \begin{verbatim}  
 http://www.unidata.ucar.edu/packages/netcdf/  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF  
   binaries into formatted ASCII text files.  
   
 \item \texttt{ncview} utility is a very convenient and quick way  
   to plot netCDF data and it runs on most OSes:  
   \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}  
 \begin{verbatim}  
 http://meteora.ucsd.edu/~pierce/ncview_home_page.html  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml}  
     
 \item MatLAB(c) and other common post-processing environments provide  
   various netCDF interfaces including:  
   \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}  
 \begin{verbatim}  
 http://mexcdf.sourceforge.net/  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml}  
   \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}  
 \begin{verbatim}  
 http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html  
 \end{verbatim}  
   \begin{rawhtml} </A> \end{rawhtml}  
 \end{itemize}  
   
926    
927  \subsection{Looking at the output}  \subsection{Looking at the output}
928    
# Line 970  Some examples of reading and visualizing Line 958  Some examples of reading and visualizing
958  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
959  they are described in Section \ref{sec:pkg:mnc}.  they are described in Section \ref{sec:pkg:mnc}.
960    
961    The MNC output files are all in the ``self-describing'' netCDF
962    format and can thus be browsed and/or plotted using tools such as:
963    \begin{itemize}
964    \item \texttt{ncdump} is a utility which is typically included
965      with every netCDF install:
966      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
967    \begin{verbatim}
968    http://www.unidata.ucar.edu/packages/netcdf/
969    \end{verbatim}
970      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
971      binaries into formatted ASCII text files.
972    
973    \item \texttt{ncview} utility is a very convenient and quick way
974      to plot netCDF data and it runs on most OSes:
975      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
976    \begin{verbatim}
977    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
978    \end{verbatim}
979      \begin{rawhtml} </A> \end{rawhtml}
980      
981    \item MatLAB(c) and other common post-processing environments provide
982      various netCDF interfaces including:
983      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
984    \begin{verbatim}
985    http://mexcdf.sourceforge.net/
986    \end{verbatim}
987      \begin{rawhtml} </A> \end{rawhtml}
988      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
989    \begin{verbatim}
990    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
991    \end{verbatim}
992      \begin{rawhtml} </A> \end{rawhtml}
993    \end{itemize}
994    
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