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revision 1.37 by molod, Wed Jun 28 16:48:19 2006 UTC revision 1.42 by jmc, Fri May 28 02:09:59 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{sect:whereToFindInfo}
# Line 104  The MITgcm web site contains further dir Line 102  The MITgcm web site contains further dir
102  code and CVS.  It also contains a web interface to our CVS archive so  code and CVS.  It also contains a web interface to our CVS archive so
103  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
104  development milestones:  development milestones:
105  \begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}  %\begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
106    \begin{rawhtml} <A href="http://mitgcm.org/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
107  \begin{verbatim}  \begin{verbatim}
108  http://mitgcm.org/source_code.html  http://mitgcm.org/source_code.html
109  \end{verbatim}  \end{verbatim}
# Line 141  track of your file versions with respect Line 140  track of your file versions with respect
140  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
141  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
142  MITgcm code can be found  MITgcm code can be found
143  \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}
144  here  here
145  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
146  .  .
# Line 225  with. So please be sure you understand w Line 224  with. So please be sure you understand w
224    
225  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
226  tar file from the web site at:  tar file from the web site at:
227  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/download/ target="idontexist"> \end{rawhtml}
228  \begin{verbatim}  \begin{verbatim}
229  http://mitgcm.org/download/  http://mitgcm.org/download/
230  \end{verbatim}  \end{verbatim}
# Line 521  To compile the code, first use the progr Line 520  To compile the code, first use the progr
520  in the \texttt{tools} directory) to generate a Makefile.  in the \texttt{tools} directory) to generate a Makefile.
521  \texttt{genmake2} is a shell script written to work with all  \texttt{genmake2} is a shell script written to work with all
522  ``sh''--compatible shells including bash v1, bash v2, and Bourne.  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
523  Internally, \texttt{genmake2} determines the locations of needed  %Internally, \texttt{genmake2} determines the locations of needed
524  files, the compiler, compiler options, libraries, and Unix tools.  It  %files, the compiler, compiler options, libraries, and Unix tools.  It
525  relies upon a number of ``optfiles'' located in the  %relies upon a number of ``optfiles'' located in the
526  \texttt{tools/build\_options} directory.  %\texttt{tools/build\_options} directory.
527    \texttt{genmake2} parses information from the following sources:
528    \begin{description}
529    \item[-] a {\em gemake\_local} file if one is found in the current
530      directory
531    \item[-] command-line options
532    \item[-] an "options file" as specified by the command-line option
533      \texttt{--optfile=/PATH/FILENAME}
534    \item[-] a {\em packages.conf} file (if one is found) with the
535      specific list of packages to compile. The search path for
536      file {\em packages.conf} is, first, the current directory and
537      then each of the "MODS" directories in the given order (see below).
538    \end{description}
539    
540    \subsubsection{Optfiles in \texttt{tools/build\_options} directory:}
541    
542  The purpose of the optfiles is to provide all the compilation options  The purpose of the optfiles is to provide all the compilation options
543  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 610  for inclusion.  Please send the file to
610  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
611  mailing list.  mailing list.
612    
613    \subsubsection{Command-line options:}
614    
615  In addition to the optfiles, \texttt{genmake2} supports a number of  In addition to the optfiles, \texttt{genmake2} supports a number of
616  helpful command-line options.  A complete list of these options can be  helpful command-line options.  A complete list of these options can be
617  obtained from:  obtained from:
# Line 619  The most important command-line options Line 634  The most important command-line options
634    the user's path.  When these three items have been identified,    the user's path.  When these three items have been identified,
635    genmake2 will try to find an optfile that has a matching name.    genmake2 will try to find an optfile that has a matching name.
636        
637  \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default  \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
638    set of packages to be used.  The normal order of precedence for    directories containing ``modifications''.  These directories contain
639    packages is as follows:    files with names that may (or may not) exist in the main MITgcm
640    \begin{enumerate}    source tree but will be overridden by any identically-named sources
641    \item If available, the command line (\texttt{--pdefault}) settings    within the ``MODS'' directories.
642      over-rule any others.    
643      The order of precedence for this "name-hiding" is as follows:
644    \item Next, \texttt{genmake2} will look for a file named    \begin{itemize}
645      ``\texttt{packages.conf}'' in the local directory or in any of the    \item ``MODS'' directories (in the order given)
646      directories specified with the \texttt{--mods} option.    \item Packages either explicitly specified or provided by default
647            (in the order given)
648    \item Finally, if neither of the above are available,    \item Packages included due to package dependencies (in the order
649      \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.      that that package dependencies are parsed)
650    \end{enumerate}    \item The "standard dirs" (which may have been specified by the
651        ``-standarddirs'' option)
652      \end{itemize}
653        
654    \item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
655      where package groups are defined. If not set, the package-groups
656      definition will be read from {\em pkg/pkg\_groups}.
657      It also contains the default list of packages (defined
658      as the group ``{\it default\_pkg\_list}'' which is used
659      when no specific package list ({\em packages.conf})
660      is found in current directory or in any "MODS" directory.
661    
662  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
663    used for packages.    used for packages.
664        
# Line 658  The most important command-line options Line 683  The most important command-line options
683    "STAF" compiler.  As with any compilers, it is helpful to have their    "STAF" compiler.  As with any compilers, it is helpful to have their
684    directories listed in your {\tt \$PATH} environment variable.    directories listed in your {\tt \$PATH} environment variable.
685        
 \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}  
     
686  \item[\texttt{--mpi}] This option enables certain MPI features (using  \item[\texttt{--mpi}] This option enables certain MPI features (using
687    CPP \texttt{\#define}s) within the code and is necessary for MPI    CPP \texttt{\#define}s) within the code and is necessary for MPI
688    builds (see Section \ref{sect:mpi-build}).    builds (see Section \ref{sect:mpi-build}).
# Line 717  The steps for building MITgcm with MPI s Line 725  The steps for building MITgcm with MPI s
725    libraries and put them into an options file as described in Section    libraries and put them into an options file as described in Section
726    \ref{sect:genmake}.  One can start with one of the examples in:    \ref{sect:genmake}.  One can start with one of the examples in:
727    \begin{rawhtml} <A    \begin{rawhtml} <A
728      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
729    \end{rawhtml}    \end{rawhtml}
730    \begin{center}    \begin{center}
731      \texttt{MITgcm/tools/build\_options/}      \texttt{MITgcm/tools/build\_options/}
# Line 768  The steps for building MITgcm with MPI s Line 776  The steps for building MITgcm with MPI s
776    library and a job scheduling and queueing system such as PBS,    library and a job scheduling and queueing system such as PBS,
777    LoadLeveller, Condor, or any of a number of similar tools.  A few    LoadLeveller, Condor, or any of a number of similar tools.  A few
778    example scripts (those used for our \begin{rawhtml} <A    example scripts (those used for our \begin{rawhtml} <A
779      href="http://mitgcm.org/testing.html"> \end{rawhtml}regular      href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
780    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
781    at:    at:
782    \begin{rawhtml} <A    \begin{rawhtml} <A
783      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/">
784      \end{rawhtml}
785      {\footnotesize \tt
786        http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
787      \begin{rawhtml} </A> \end{rawhtml}
788      or at:
789      \begin{rawhtml} <A
790        href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
791    \end{rawhtml}    \end{rawhtml}
792    {\footnotesize \tt    {\footnotesize \tt
793      http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }      http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
794    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
795    
796  \end{enumerate}  \end{enumerate}
# Line 894  as the pickup files but are named differ Line 909  as the pickup files but are named differ
909  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
910  output to save disk space during long integrations.  output to save disk space during long integrations.
911    
   
   
912  \subsubsection{MNC output files}  \subsubsection{MNC output files}
913    
914  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
915  is usually (though not necessarily) placed within a subdirectory with  is usually (though not necessarily) placed within a subdirectory with
916  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}  
   
917    
918  \subsection{Looking at the output}  \subsection{Looking at the output}
919    
# Line 970  Some examples of reading and visualizing Line 949  Some examples of reading and visualizing
949  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
950  they are described in Section \ref{sec:pkg:mnc}.  they are described in Section \ref{sec:pkg:mnc}.
951    
952    The MNC output files are all in the ``self-describing'' netCDF
953    format and can thus be browsed and/or plotted using tools such as:
954    \begin{itemize}
955    \item \texttt{ncdump} is a utility which is typically included
956      with every netCDF install:
957      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
958    \begin{verbatim}
959    http://www.unidata.ucar.edu/packages/netcdf/
960    \end{verbatim}
961      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
962      binaries into formatted ASCII text files.
963    
964    \item \texttt{ncview} utility is a very convenient and quick way
965      to plot netCDF data and it runs on most OSes:
966      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
967    \begin{verbatim}
968    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
969    \end{verbatim}
970      \begin{rawhtml} </A> \end{rawhtml}
971      
972    \item MatLAB(c) and other common post-processing environments provide
973      various netCDF interfaces including:
974      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
975    \begin{verbatim}
976    http://mexcdf.sourceforge.net/
977    \end{verbatim}
978      \begin{rawhtml} </A> \end{rawhtml}
979      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
980    \begin{verbatim}
981    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
982    \end{verbatim}
983      \begin{rawhtml} </A> \end{rawhtml}
984    \end{itemize}
985    
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