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revision 1.27 by cnh, Thu Oct 14 14:24:28 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 561  where we are re-directing the stream of Line 565  where we are re-directing the stream of
565  output.txt}.  output.txt}.
566    
567    
 \subsection{Building/compiling the code elsewhere}  
   
 In the example above (section \ref{sect:buildingCode}) we built the  
 executable in the {\em input} directory of the experiment for  
 convenience. You can also configure and compile the code in other  
 locations, for example on a scratch disk with out having to copy the  
 entire source tree. The only requirement to do so is you have {\tt  
   genmake2} in your path or you know the absolute path to {\tt  
   genmake2}.  
   
 The following sections outline some possible methods of organizing  
 your source and data.  
   
 \subsubsection{Building from the {\em ../code directory}}  
   
 This is just as simple as building in the {\em input/} directory:  
 \begin{verbatim}  
 % cd verification/exp2/code  
 % ../../../tools/genmake2  
 % make depend  
 % make  
 \end{verbatim}  
 However, to run the model the executable ({\em mitgcmuv}) and input  
 files must be in the same place. If you only have one calculation to make:  
 \begin{verbatim}  
 % cd ../input  
 % cp ../code/mitgcmuv ./  
 % ./mitgcmuv > output.txt  
 \end{verbatim}  
 or if you will be making multiple runs with the same executable:  
 \begin{verbatim}  
 % cd ../  
 % cp -r input run1  
 % cp code/mitgcmuv run1  
 % cd run1  
 % ./mitgcmuv > output.txt  
 \end{verbatim}  
   
 \subsubsection{Building from a new directory}  
   
 Since the {\em input} directory contains input files it is often more  
 useful to keep {\em input} pristine and build in a new directory  
 within {\em verification/exp2/}:  
 \begin{verbatim}  
 % cd verification/exp2  
 % mkdir build  
 % cd build  
 % ../../../tools/genmake2 -mods=../code  
 % make depend  
 % make  
 \end{verbatim}  
 This builds the code exactly as before but this time you need to copy  
 either the executable or the input files or both in order to run the  
 model. For example,  
 \begin{verbatim}  
 % cp ../input/* ./  
 % ./mitgcmuv > output.txt  
 \end{verbatim}  
 or if you tend to make multiple runs with the same executable then  
 running in a new directory each time might be more appropriate:  
 \begin{verbatim}  
 % cd ../  
 % mkdir run1  
 % cp build/mitgcmuv run1/  
 % cp input/* run1/  
 % cd run1  
 % ./mitgcmuv > output.txt  
 \end{verbatim}  
   
 \subsubsection{Building on a scratch disk}  
   
 Model object files and output data can use up large amounts of disk  
 space so it is often the case that you will be operating on a large  
 scratch disk. Assuming the model source is in {\em ~/MITgcm} then the  
 following commands will build the model in {\em /scratch/exp2-run1}:  
 \begin{verbatim}  
 % cd /scratch/exp2-run1  
 % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \  
   -mods=~/MITgcm/verification/exp2/code  
 % make depend  
 % make  
 \end{verbatim}  
 To run the model here, you'll need the input files:  
 \begin{verbatim}  
 % cp ~/MITgcm/verification/exp2/input/* ./  
 % ./mitgcmuv > output.txt  
 \end{verbatim}  
   
 As before, you could build in one directory and make multiple runs of  
 the one experiment:  
 \begin{verbatim}  
 % cd /scratch/exp2  
 % mkdir build  
 % cd build  
 % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \  
   -mods=~/MITgcm/verification/exp2/code  
 % make depend  
 % make  
 % cd ../  
 % cp -r ~/MITgcm/verification/exp2/input run2  
 % cd run2  
 % ./mitgcmuv > output.txt  
 \end{verbatim}  
   
   
 \subsection{Using \texttt{genmake2}}  
 \label{sect:genmake}  
   
 To compile the code, first use the program \texttt{genmake2} (located  
 in the \texttt{tools} directory) to generate a Makefile.  
 \texttt{genmake2} is a shell script written to work with all  
 ``sh''--compatible shells including bash v1, bash v2, and Bourne.  
 Internally, \texttt{genmake2} determines the locations of needed  
 files, the compiler, compiler options, libraries, and Unix tools.  It  
 relies upon a number of ``optfiles'' located in the  
 \texttt{tools/build\_options} directory.  
   
 The purpose of the optfiles is to provide all the compilation options  
 for particular ``platforms'' (where ``platform'' roughly means the  
 combination of the hardware and the compiler) and code configurations.  
 Given the combinations of possible compilers and library dependencies  
 ({\it eg.}  MPI and NetCDF) there may be numerous optfiles available  
 for a single machine.  The naming scheme for the majority of the  
 optfiles shipped with the code is  
 \begin{center}  
   {\bf OS\_HARDWARE\_COMPILER }  
 \end{center}  
 where  
 \begin{description}  
 \item[OS] is the name of the operating system (generally the  
   lower-case output of the {\tt 'uname'} command)  
 \item[HARDWARE] is a string that describes the CPU type and  
   corresponds to output from the  {\tt 'uname -m'} command:  
   \begin{description}  
   \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,  
     and athlon  
   \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)  
   \item[amd64] is AMD x86\_64 systems  
   \item[ppc] is for Mac PowerPC systems  
   \end{description}  
 \item[COMPILER] is the compiler name (generally, the name of the  
   FORTRAN executable)  
 \end{description}  
   
 In many cases, the default optfiles are sufficient and will result in  
 usable Makefiles.  However, for some machines or code configurations,  
 new ``optfiles'' must be written. To create a new optfile, it is  
 generally best to start with one of the defaults and modify it to suit  
 your needs.  Like \texttt{genmake2}, the optfiles are all written  
 using a simple ``sh''--compatible syntax.  While nearly all variables  
 used within \texttt{genmake2} may be specified in the optfiles, the  
 critical ones that should be defined are:  
   
 \begin{description}  
 \item[FC] the FORTRAN compiler (executable) to use  
 \item[DEFINES] the command-line DEFINE options passed to the compiler  
 \item[CPP] the C pre-processor to use  
 \item[NOOPTFLAGS] options flags for special files that should not be  
   optimized  
 \end{description}  
   
 For example, the optfile for a typical Red Hat Linux machine (``ia32''  
 architecture) using the GCC (g77) compiler is  
 \begin{verbatim}  
 FC=g77  
 DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'  
 CPP='cpp  -traditional -P'  
 NOOPTFLAGS='-O0'  
 #  For IEEE, use the "-ffloat-store" option  
 if test "x$IEEE" = x ; then  
     FFLAGS='-Wimplicit -Wunused -Wuninitialized'  
     FOPTIM='-O3 -malign-double -funroll-loops'  
 else  
     FFLAGS='-Wimplicit -Wunused -ffloat-store'  
     FOPTIM='-O0 -malign-double'  
 fi  
 \end{verbatim}  
   
 If you write an optfile for an unrepresented machine or compiler, you  
 are strongly encouraged to submit the optfile to the MITgcm project  
 for inclusion.  Please send the file to the  
 \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}  
 \begin{center}  
   MITgcm-support@mitgcm.org  
 \end{center}  
 \begin{rawhtml} </A> \end{rawhtml}  
 mailing list.  
   
 In addition to the optfiles, \texttt{genmake2} supports a number of  
 helpful command-line options.  A complete list of these options can be  
 obtained from:  
 \begin{verbatim}  
 % genmake2 -h  
 \end{verbatim}  
   
 The most important command-line options are:  
 \begin{description}  
     
 \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that  
   should be used for a particular build.  
     
   If no "optfile" is specified (either through the command line or the  
   MITGCM\_OPTFILE environment variable), genmake2 will try to make a  
   reasonable guess from the list provided in {\em  
     tools/build\_options}.  The method used for making this guess is  
   to first determine the combination of operating system and hardware  
   (eg. "linux\_ia32") and then find a working FORTRAN compiler within  
   the user's path.  When these three items have been identified,  
   genmake2 will try to find an optfile that has a matching name.  
     
 \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default  
   set of packages to be used.  The normal order of precedence for  
   packages is as follows:  
   \begin{enumerate}  
   \item If available, the command line (\texttt{--pdefault}) settings  
     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}  
     
 \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file  
   used for packages.  
     
   If not specified, the default dependency file {\em pkg/pkg\_depend}  
   is used.  The syntax for this file is parsed on a line-by-line basis  
   where each line containes either a comment ("\#") or a simple  
   "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol  
   specifies a "must be used with" or a "must not be used with"  
   relationship, respectively.  If no rule is specified, then it is  
   assumed that the two packages are compatible and will function  
   either with or without each other.  
     
 \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or  
   automatic differentiation options file to be used.  The file is  
   analogous to the ``optfile'' defined above but it specifies  
   information for the AD build process.  
     
   The default file is located in {\em  
     tools/adjoint\_options/adjoint\_default} and it defines the "TAF"  
   and "TAMC" compilers.  An alternate version is also available at  
   {\em tools/adjoint\_options/adjoint\_staf} that selects the newer  
   "STAF" compiler.  As with any compilers, it is helpful to have their  
   directories listed in your {\tt \$PATH} environment variable.  
     
 \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}  
     
 \item[\texttt{--mpi}] This option enables certain MPI features (using  
   CPP \texttt{\#define}s) within the code and is necessary for MPI  
   builds (see Section \ref{sect:mpi-build}).  
     
 \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of  
   soft-links and other bugs common with the \texttt{make} versions  
   provided by commercial Unix vendors, GNU \texttt{make} (sometimes  
   called \texttt{gmake}) should be preferred.  This option provides a  
   means for specifying the make executable to be used.  
     
 \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)  
   machines, the ``bash'' shell is unavailable.  To run on these  
   systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,  
   a Bourne, POSIX, or compatible) shell.  The syntax in these  
   circumstances is:  
   \begin{center}  
     \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}  
   \end{center}  
   where \texttt{/bin/sh} can be replaced with the full path and name  
   of the desired shell.  
   
 \end{description}  
   
   
 \subsection{Building with MPI}  
 \label{sect:mpi-build}  
   
 Building MITgcm to use MPI libraries can be complicated due to the  
 variety of different MPI implementations available, their dependencies  
 or interactions with different compilers, and their often ad-hoc  
 locations within file systems.  For these reasons, its generally a  
 good idea to start by finding and reading the documentation for your  
 machine(s) and, if necessary, seeking help from your local systems  
 administrator.  
   
 The steps for building MITgcm with MPI support are:  
 \begin{enumerate}  
     
 \item Determine the locations of your MPI-enabled compiler and/or MPI  
   libraries and put them into an options file as described in Section  
   \ref{sect:genmake}.  One can start with one of the examples in:  
   \begin{rawhtml} <A  
     href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">  
   \end{rawhtml}  
   \begin{center}  
     \texttt{MITgcm/tools/build\_options/}  
   \end{center}  
   \begin{rawhtml} </A> \end{rawhtml}  
   such as \texttt{linux\_ia32\_g77+mpi\_cg01} or  
   \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at  
   hand.  You may need help from your user guide or local systems  
   administrator to determine the exact location of the MPI libraries.  
   If libraries are not installed, MPI implementations and related  
   tools are available including:  
   \begin{itemize}  
   \item \begin{rawhtml} <A  
       href="http://www-unix.mcs.anl.gov/mpi/mpich/">  
     \end{rawhtml}  
     MPICH  
     \begin{rawhtml} </A> \end{rawhtml}  
   
   \item \begin{rawhtml} <A  
       href="http://www.lam-mpi.org/">  
     \end{rawhtml}  
     LAM/MPI  
     \begin{rawhtml} </A> \end{rawhtml}  
   
   \item \begin{rawhtml} <A  
       href="http://www.osc.edu/~pw/mpiexec/">  
     \end{rawhtml}  
     MPIexec  
     \begin{rawhtml} </A> \end{rawhtml}  
   \end{itemize}  
     
 \item Build the code with the \texttt{genmake2} \texttt{-mpi} option  
   (see Section \ref{sect:genmake}) using commands such as:  
 {\footnotesize \begin{verbatim}  
   %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE  
   %  make depend  
   %  make  
 \end{verbatim} }  
     
 \item Run the code with the appropriate MPI ``run'' or ``exec''  
   program provided with your particular implementation of MPI.  
   Typical MPI packages such as MPICH will use something like:  
 \begin{verbatim}  
   %  mpirun -np 4 -machinefile mf ./mitgcmuv  
 \end{verbatim}  
   Sightly more complicated scripts may be needed for many machines  
   since execution of the code may be controlled by both the MPI  
   library and a job scheduling and queueing system such as PBS,  
   LoadLeveller, Condor, or any of a number of similar tools.  A few  
   example scripts (those used for our \begin{rawhtml} <A  
     href="http://mitgcm.org/testing.html"> \end{rawhtml}regular  
   verification runs\begin{rawhtml} </A> \end{rawhtml}) are available  
   at:  
   \begin{rawhtml} <A  
     href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">  
   \end{rawhtml}  
   {\footnotesize \tt  
     http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }  
   \begin{rawhtml} </A> \end{rawhtml}  
   
 \end{enumerate}  
   
 An example of the above process on the MITgcm cluster (``cg01'') using  
 the GNU g77 compiler and the mpich MPI library is:  
   
 {\footnotesize \begin{verbatim}  
   %  cd MITgcm/verification/exp5  
   %  mkdir build  
   %  cd build  
   %  ../../../tools/genmake2 -mpi -mods=../code \  
        -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01  
   %  make depend  
   %  make  
   %  cd ../input  
   %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \  
        -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv  
 \end{verbatim} }  
   
   
   
568  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
569  \label{sect:runModel}  \label{sect:runModel}
570    
# Line 957  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 972  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 1030  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 1059  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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