/[MITgcm]/manual/s_getstarted/text/getting_started.tex
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revision 1.28 by cnh, Thu Oct 14 14:54:24 2004 UTC revision 1.29 by edhill, Thu Oct 14 19:11:47 2004 UTC
# Line 507  First, build the {\em Makefile}: Line 507  First, build the {\em Makefile}:
507  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
508  \end{verbatim}  \end{verbatim}
509  The command line option tells {\em genmake} to override model source  The command line option tells {\em genmake} to override model source
510  code with any files in the directory {\em ./code/}.  code with any files in the directory {\em ../code/}.
511    
512  On many systems, the {\em genmake2} program will be able to  On many systems, the {\em genmake2} program will be able to
513  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
514  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``echo \$PATH''), and then choose an
515  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
516    tools/build\_options} directory.  Under some circumstances, a user  the {\em tools/build\_options} directory.  Under some circumstances, a
517  may have to create a new ``optfile'' in order to specify the exact  user may have to create a new ``optfile'' in order to specify the
518  combination of compiler, compiler flags, libraries, and other options  exact combination of compiler, compiler flags, libraries, and other
519  necessary to build a particular configuration of MITgcm.  In such  options necessary to build a particular configuration of MITgcm.  In
520  cases, it is generally helpful to read the existing ``optfiles'' and  such cases, it is generally helpful to read the existing ``optfiles''
521  mimic their syntax.  and mimic their syntax.
522    
523  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
524  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
# Line 542  This modifies the {\em Makefile} by atta Line 542  This modifies the {\em Makefile} by atta
542  upon which other files depend. The purpose of this is to reduce  upon which other files depend. The purpose of this is to reduce
543  re-compilation if and when you start to modify the code. The {\tt make  re-compilation if and when you start to modify the code. The {\tt make
544    depend} command also creates links from the model source to this    depend} command also creates links from the model source to this
545  directory.  directory.  It is important to note that the {\tt make depend} stage
546    will occasionally produce warnings or errors since the dependency
547    parsing tool is unable to find all of the necessary header files
548    (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it is
549    usually OK to ignore the warnings/errors and proceed to the next step.
550    
551  Next compile the code:  Next compile the code:
552  \begin{verbatim}  \begin{verbatim}
# Line 568  If compilation finished succesfuully (se Line 572  If compilation finished succesfuully (se
572  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
573  local directory.  local directory.
574    
575  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)
576  type:  simply type:
577  \begin{verbatim}  \begin{verbatim}
578  % ./mitgcmuv  % ./mitgcmuv
579  \end{verbatim}  \end{verbatim}
# Line 583  normally re-direct the {\em stdout} stre Line 587  normally re-direct the {\em stdout} stre
587  \begin{verbatim}  \begin{verbatim}
588  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
589  \end{verbatim}  \end{verbatim}
590    In the event that the model encounters an error and stops, it is very
591    helpful to include the last few line of this \texttt{output.txt} file
592    along with the (\texttt{stderr}) error message within any bug reports.
593    
594  For the example experiments in {\em verification}, an example of the  For the example experiments in {\em verification}, an example of the
595  output is kept in {\em results/output.txt} for comparison. You can compare  output is kept in {\em results/output.txt} for comparison. You can
596  your {\em output.txt} with this one to check that the set-up works.  compare your {\em output.txt} with the corresponding one for that
597    experiment to check that the set-up works.
598    
599    
600    
601  \subsection{Output files}  \subsection{Output files}
602    
603  The model produces various output files. At a minimum, the instantaneous  The model produces various output files.  Depending upon the I/O
604  ``state'' of the model is written out, which is made of the following files:  package selected (either \texttt{mdsio} or \texttt{mnc} or both as
605    determined by both the compile-time settings and the run-time flags in
606    \texttt{data.pkg}), the following output may appear.
607    
608    
609    \subsubsection{MDSIO output files}
610    
611    The ``traditional'' output files are generated by the \texttt{mdsio}
612    package.  At a minimum, the instantaneous ``state'' of the model is
613    written out, which is made of the following files:
614    
615  \begin{itemize}  \begin{itemize}
616  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>
# Line 641  as the pickup files but are named differ Line 658  as the pickup files but are named differ
658  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
659  output to save disk space during long integrations.  output to save disk space during long integrations.
660    
661    
662    
663    \subsubsection{MNC output files}
664    
665    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
666    is usually (though not necessarily) placed within a subdirectory with
667    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files
668    within this subdirectory are all in the ``self-describing'' netCDF
669    format and can thus be browsed and/or plotted using tools such as:
670    \begin{itemize}
671    \item At a minimum, the \texttt{ncdump} utility is typically included
672      with every netCDF install:
673      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
674    \begin{verbatim}
675    http://www.unidata.ucar.edu/packages/netcdf/
676    \end{verbatim}
677      \begin{rawhtml} </A> \end{rawhtml}
678    
679    \item The \texttt{ncview} utility is a very convenient and quick way
680      to plot netCDF data and it runs on most OSes:
681      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
682    \begin{verbatim}
683    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
684    \end{verbatim}
685      \begin{rawhtml} </A> \end{rawhtml}
686      
687    \item MatLAB(c) and other common post-processing environments provide
688      various netCDF interfaces including:
689      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
690    \begin{verbatim}
691    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
692    \end{verbatim}
693      \begin{rawhtml} </A> \end{rawhtml}
694    
695    \end{itemize}
696    
697    
698  \subsection{Looking at the output}  \subsection{Looking at the output}
699    
700  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
701  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
702  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \textit{.data} and \textit{.meta}. The
703  binary form (big\_endian by default). The \textit{.meta} file is a  \textit{.data} file contains the data written in binary form
704  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \textit{.meta} file is a ``header'' file
705  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
706  particularly useful when running multi-processors calculations. The base  \textit{.data} file. This way of organizing the output is particularly
707  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
708  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
709  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
710  the data. Look at the comments inside the script to see how to use it.  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m}
711    reads the data. Look at the comments inside the script to see how to
712    use it.
713    
714  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
715  \begin{verbatim}  \begin{verbatim}
# Line 670  Some examples of reading and visualizing Line 726  Some examples of reading and visualizing
726  >> 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
727  \end{verbatim}  \end{verbatim}
728    
729    Similar scripts for netCDF output (\texttt{rdmnc.m}) are available.
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