/[MITgcm]/manual/s_getstarted/text/getting_started.tex
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revision 1.39 by molod, Fri Jun 30 15:56:52 2006 UTC revision 1.43 by jmc, Fri May 28 21:04:18 2010 UTC
# Line 102  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 139  track of your file versions with respect Line 139  track of your file versions with respect
139  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
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 223  with. So please be sure you understand w Line 223  with. So please be sure you understand w
223    
224  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
225  tar file from the web site at:  tar file from the web site at:
226  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/download/ target="idontexist"> \end{rawhtml}
227  \begin{verbatim}  \begin{verbatim}
228  http://mitgcm.org/download/  http://mitgcm.org/download/
229  \end{verbatim}  \end{verbatim}
# Line 519  To compile the code, first use the progr Line 519  To compile the code, first use the progr
519  in the \texttt{tools} directory) to generate a Makefile.  in the \texttt{tools} directory) to generate a Makefile.
520  \texttt{genmake2} is a shell script written to work with all  \texttt{genmake2} is a shell script written to work with all
521  ``sh''--compatible shells including bash v1, bash v2, and Bourne.  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
522  Internally, \texttt{genmake2} determines the locations of needed  %Internally, \texttt{genmake2} determines the locations of needed
523  files, the compiler, compiler options, libraries, and Unix tools.  It  %files, the compiler, compiler options, libraries, and Unix tools.  It
524  relies upon a number of ``optfiles'' located in the  %relies upon a number of ``optfiles'' located in the
525  \texttt{tools/build\_options} directory.  %\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  The purpose of the optfiles is to provide all the compilation options
542  for particular ``platforms'' (where ``platform'' roughly means the  for particular ``platforms'' (where ``platform'' roughly means the
# Line 595  for inclusion.  Please send the file to Line 609  for inclusion.  Please send the file to
609  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
610  mailing list.  mailing list.
611    
612    \subsubsection{Command-line options:}
613    
614  In addition to the optfiles, \texttt{genmake2} supports a number of  In addition to the optfiles, \texttt{genmake2} supports a number of
615  helpful command-line options.  A complete list of these options can be  helpful command-line options.  A complete list of these options can be
616  obtained from:  obtained from:
# Line 617  The most important command-line options Line 633  The most important command-line options
633    the user's path.  When these three items have been identified,    the user's path.  When these three items have been identified,
634    genmake2 will try to find an optfile that has a matching name.    genmake2 will try to find an optfile that has a matching name.
635        
636  \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default  \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
637    set of packages to be used.  The normal order of precedence for    directories containing ``modifications''.  These directories contain
638    packages is as follows:    files with names that may (or may not) exist in the main MITgcm
639    \begin{enumerate}    source tree but will be overridden by any identically-named sources
640    \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}  
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  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
662    used for packages.    used for packages.
663        
# Line 656  The most important command-line options Line 682  The most important command-line options
682    "STAF" compiler.  As with any compilers, it is helpful to have their    "STAF" compiler.  As with any compilers, it is helpful to have their
683    directories listed in your {\tt \$PATH} environment variable.    directories listed in your {\tt \$PATH} environment variable.
684        
 \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}  
     
685  \item[\texttt{--mpi}] This option enables certain MPI features (using  \item[\texttt{--mpi}] This option enables certain MPI features (using
686    CPP \texttt{\#define}s) within the code and is necessary for MPI    CPP \texttt{\#define}s) within the code and is necessary for MPI
687    builds (see Section \ref{sect:mpi-build}).    builds (see Section \ref{sect:mpi-build}).
# Line 715  The steps for building MITgcm with MPI s Line 724  The steps for building MITgcm with MPI s
724    libraries and put them into an options file as described in Section    libraries and put them into an options file as described in Section
725    \ref{sect:genmake}.  One can start with one of the examples in:    \ref{sect:genmake}.  One can start with one of the examples in:
726    \begin{rawhtml} <A    \begin{rawhtml} <A
727      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
728    \end{rawhtml}    \end{rawhtml}
729    \begin{center}    \begin{center}
730      \texttt{MITgcm/tools/build\_options/}      \texttt{MITgcm/tools/build\_options/}
# Line 766  The steps for building MITgcm with MPI s Line 775  The steps for building MITgcm with MPI s
775    library and a job scheduling and queueing system such as PBS,    library and a job scheduling and queueing system such as PBS,
776    LoadLeveller, Condor, or any of a number of similar tools.  A few    LoadLeveller, Condor, or any of a number of similar tools.  A few
777    example scripts (those used for our \begin{rawhtml} <A    example scripts (those used for our \begin{rawhtml} <A
778      href="http://mitgcm.org/testing.html"> \end{rawhtml}regular      href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
779    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available    verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
780    at:    at:
781    \begin{rawhtml} <A    \begin{rawhtml} <A
782      href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">      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}    \end{rawhtml}
791    {\footnotesize \tt    {\footnotesize \tt
792      http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }      http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
793    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
794    
795  \end{enumerate}  \end{enumerate}
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