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revision 1.27 by cnh, Thu Oct 14 14:24:28 2004 UTC revision 1.30 by edhill, Sat Oct 16 03:40:13 2004 UTC
# Line 15  structure are described more fully in ch Line 15  structure are described more fully in ch
15  this section, we provide information on how to customize the code when  this section, we provide information on how to customize the code when
16  you are ready to try implementing the configuration you have in mind.  you are ready to try implementing the configuration you have in mind.
17    
18    
19  \section{Where to find information}  \section{Where to find information}
20  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
21    \begin{rawhtml}
22    <!-- CMIREDIR:whereToFindInfo: -->
23    \end{rawhtml}
24    
25  A web site is maintained for release 2 (``Pelican'') of MITgcm:  A web site is maintained for release 2 (``Pelican'') of MITgcm:
26  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
# Line 50  http://mitgcm.org/htdig/ Line 54  http://mitgcm.org/htdig/
54    
55  \section{Obtaining the code}  \section{Obtaining the code}
56  \label{sect:obtainingCode}  \label{sect:obtainingCode}
57    \begin{rawhtml}
58    <!-- CMIREDIR:obtainingCode: -->
59    \end{rawhtml}
60    
61  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
62  the instructions below. As a courtesy we ask that you send e-mail to us at  the instructions below. As a courtesy we ask that you send e-mail to us at
# Line 256  also means we can't tell what version of Line 263  also means we can't tell what version of
263  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
264    
265  \section{Model and directory structure}  \section{Model and directory structure}
266    \begin{rawhtml}
267    <!-- CMIREDIR:directory_structure: -->
268    \end{rawhtml}
269    
270  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
271  support wrapper. This wrapper is designed to provide a general  support wrapper. This wrapper is designed to provide a general
# Line 326  structure). Line 336  structure).
336    
337  \section[MITgcm Example Experiments]{Example experiments}  \section[MITgcm Example Experiments]{Example experiments}
338  \label{sect:modelExamples}  \label{sect:modelExamples}
339    \begin{rawhtml}
340    <!-- CMIREDIR:modelExamples: -->
341    \end{rawhtml}
342    
343  %% a set of twenty-four pre-configured numerical experiments  %% a set of twenty-four pre-configured numerical experiments
344    
# Line 486  compile the code. Line 499  compile the code.
499    
500  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
501  \label{sect:buildingCode}  \label{sect:buildingCode}
502    \begin{rawhtml}
503    <!-- CMIREDIR:buildingCode: -->
504    \end{rawhtml}
505    
506  To compile the code, we use the {\em make} program. This uses a file  To compile the code, we use the {\em make} program. This uses a file
507  ({\em Makefile}) that allows us to pre-process source files, specify  ({\em Makefile}) that allows us to pre-process source files, specify
# Line 507  First, build the {\em Makefile}: Line 523  First, build the {\em Makefile}:
523  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
524  \end{verbatim}  \end{verbatim}
525  The command line option tells {\em genmake} to override model source  The command line option tells {\em genmake} to override model source
526  code with any files in the directory {\em ./code/}.  code with any files in the directory {\em ../code/}.
527    
528  On many systems, the {\em genmake2} program will be able to  On many systems, the {\em genmake2} program will be able to
529  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
530  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``echo \$PATH''), and then choose an
531  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
532    tools/build\_options} directory.  Under some circumstances, a user  the {\em tools/build\_options} directory.  Under some circumstances, a
533  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
534  combination of compiler, compiler flags, libraries, and other options  exact combination of compiler, compiler flags, libraries, and other
535  necessary to build a particular configuration of MITgcm.  In such  options necessary to build a particular configuration of MITgcm.  In
536  cases, it is generally helpful to read the existing ``optfiles'' and  such cases, it is generally helpful to read the existing ``optfiles''
537  mimic their syntax.  and mimic their syntax.
538    
539  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
540  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 558  This modifies the {\em Makefile} by atta
558  upon which other files depend. The purpose of this is to reduce  upon which other files depend. The purpose of this is to reduce
559  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
560    depend} command also creates links from the model source to this    depend} command also creates links from the model source to this
561  directory.  directory.  It is important to note that the {\tt make depend} stage
562    will occasionally produce warnings or errors since the dependency
563    parsing tool is unable to find all of the necessary header files
564    (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it is
565    usually OK to ignore the warnings/errors and proceed to the next step.
566    
567  Next compile the code:  Next compile the code:
568  \begin{verbatim}  \begin{verbatim}
# Line 561  where we are re-directing the stream of Line 581  where we are re-directing the stream of
581  output.txt}.  output.txt}.
582    
583    
 \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} }  
   
   
   
584  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
585  \label{sect:runModel}  \label{sect:runModel}
586    \begin{rawhtml}
587    <!-- CMIREDIR:runModel: -->
588    \end{rawhtml}
589    
590  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfuully (section \ref{sect:buildingCode})
591  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
592  local directory.  local directory.
593    
594  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)
595  type:  simply type:
596  \begin{verbatim}  \begin{verbatim}
597  % ./mitgcmuv  % ./mitgcmuv
598  \end{verbatim}  \end{verbatim}
# Line 972  normally re-direct the {\em stdout} stre Line 606  normally re-direct the {\em stdout} stre
606  \begin{verbatim}  \begin{verbatim}
607  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
608  \end{verbatim}  \end{verbatim}
609    In the event that the model encounters an error and stops, it is very
610    helpful to include the last few line of this \texttt{output.txt} file
611    along with the (\texttt{stderr}) error message within any bug reports.
612    
613  For the example experiments in {\em verification}, an example of the  For the example experiments in {\em verification}, an example of the
614  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
615  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
616    experiment to check that the set-up works.
617    
618    
619    
620  \subsection{Output files}  \subsection{Output files}
621    
622  The model produces various output files. At a minimum, the instantaneous  The model produces various output files.  Depending upon the I/O
623  ``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
624    determined by both the compile-time settings and the run-time flags in
625    \texttt{data.pkg}), the following output may appear.
626    
627    
628    \subsubsection{MDSIO output files}
629    
630    The ``traditional'' output files are generated by the \texttt{mdsio}
631    package.  At a minimum, the instantaneous ``state'' of the model is
632    written out, which is made of the following files:
633    
634  \begin{itemize}  \begin{itemize}
635  \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 677  as the pickup files but are named differ
677  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
678  output to save disk space during long integrations.  output to save disk space during long integrations.
679    
680    
681    
682    \subsubsection{MNC output files}
683    
684    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
685    is usually (though not necessarily) placed within a subdirectory with
686    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files
687    within this subdirectory are all in the ``self-describing'' netCDF
688    format and can thus be browsed and/or plotted using tools such as:
689    \begin{itemize}
690    \item At a minimum, the \texttt{ncdump} utility is typically included
691      with every netCDF install:
692      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
693    \begin{verbatim}
694    http://www.unidata.ucar.edu/packages/netcdf/
695    \end{verbatim}
696      \begin{rawhtml} </A> \end{rawhtml}
697    
698    \item The \texttt{ncview} utility is a very convenient and quick way
699      to plot netCDF data and it runs on most OSes:
700      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
701    \begin{verbatim}
702    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
703    \end{verbatim}
704      \begin{rawhtml} </A> \end{rawhtml}
705      
706    \item MatLAB(c) and other common post-processing environments provide
707      various netCDF interfaces including:
708      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
709    \begin{verbatim}
710    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
711    \end{verbatim}
712      \begin{rawhtml} </A> \end{rawhtml}
713    
714    \end{itemize}
715    
716    
717  \subsection{Looking at the output}  \subsection{Looking at the output}
718    
719  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
720  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
721  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \textit{.data} and \textit{.meta}. The
722  binary form (big\_endian by default). The \textit{.meta} file is a  \textit{.data} file contains the data written in binary form
723  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \textit{.meta} file is a ``header'' file
724  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
725  particularly useful when running multi-processors calculations. The base  \textit{.data} file. This way of organizing the output is particularly
726  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
727  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
728  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
729  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}
730    reads the data. Look at the comments inside the script to see how to
731    use it.
732    
733  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
734  \begin{verbatim}  \begin{verbatim}
# Line 1059  Some examples of reading and visualizing Line 745  Some examples of reading and visualizing
745  >> 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
746  \end{verbatim}  \end{verbatim}
747    
748    Similar scripts for netCDF output (\texttt{rdmnc.m}) are available.
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