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revision 1.31 by edhill, Tue Aug 9 21:52:09 2005 UTC revision 1.36 by molod, Tue Jun 27 19:08:22 2006 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  \section{Where to find information}  \section{Where to find information}
19  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
20  \begin{rawhtml}  \begin{rawhtml}
# Line 126  The MITgcm web site contains further dir Line 125  The MITgcm web site contains further dir
125  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
126  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
127  development milestones:  development milestones:
128  \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
129  \begin{verbatim}  \begin{verbatim}
130  http://mitgcm.org/source_code.html  http://mitgcm.org/source_code.html
131  \end{verbatim}  \end{verbatim}
# Line 163  track of your file versions with respect Line 162  track of your file versions with respect
162  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
163  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
164  MITgcm code can be found  MITgcm code can be found
165  \begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/usingcvstoget.html" target="idontexist"> \end{rawhtml}
166  here  here
167  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
168  .  .
# Line 192  delete; even if you do not use CVS yours Line 191  delete; even if you do not use CVS yours
191  us if you should need to send us your copy of the code.  If a recent  us if you should need to send us your copy of the code.  If a recent
192  tar file does not exist, then please contact the developers through  tar file does not exist, then please contact the developers through
193  the  the
194  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
195  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
196  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
197  mailing list.  mailing list.
# Line 335  structure). Line 334  structure).
334    
335  \end{itemize}  \end{itemize}
336    
 \section[MITgcm Example Experiments]{Example experiments}  
 \label{sect:modelExamples}  
 \begin{rawhtml}  
 <!-- CMIREDIR:modelExamples: -->  
 \end{rawhtml}  
   
 %% a set of twenty-four pre-configured numerical experiments  
   
 The MITgcm distribution comes with more than a dozen pre-configured  
 numerical experiments. Some of these example experiments are tests of  
 individual parts of the model code, but many are fully fledged  
 numerical simulations. A few of the examples are used for tutorial  
 documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.  
 The other examples follow the same general structure as the tutorial  
 examples. However, they only include brief instructions in a text file  
 called {\it README}.  The examples are located in subdirectories under  
 the directory \texttt{verification}. Each example is briefly described  
 below.  
   
 \subsection{Full list of model examples}  
   
 \begin{enumerate}  
     
 \item \texttt{exp0} - single layer, ocean double gyre (barotropic with  
   free-surface). This experiment is described in detail in section  
   \ref{sect:eg-baro}.  
   
 \item \texttt{exp1} - Four layer, ocean double gyre. This experiment  
   is described in detail in section \ref{sect:eg-baroc}.  
     
 \item \texttt{exp2} - 4x4 degree global ocean simulation with steady  
   climatological forcing. This experiment is described in detail in  
   section \ref{sect:eg-global}.  
     
 \item \texttt{exp4} - Flow over a Gaussian bump in open-water or  
   channel with open boundaries.  
     
 \item \texttt{exp5} - Inhomogenously forced ocean convection in a  
   doubly periodic box.  
   
 \item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for  
 Gent/McWilliams scheme). 2D (Y-Z).  
   
 \item \texttt{internal wave} - Ocean internal wave forced by open  
   boundary conditions.  
     
 \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP  
   scheme; 1 month integration  
     
 \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and  
   Suarez '94 forcing.  
     
 \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing.  
     
 \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing on the cubed sphere.  
     
 \item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  
   Global Zonal Mean configuration, 1x64x5 resolution.  
     
 \item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate  
   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).  
     
 \item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  
   physics. 3D Equatorial Channel configuration.  
     
 \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.  
   Global configuration, on latitude longitude grid with 128x64x5 grid  
   points ($2.8^\circ{\rm degree}$ resolution).  
     
 \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on  
   latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on  
   cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \texttt{advect\_cs} Two-dimensional passive advection test on  
   cube sphere grid.  
     
 \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive  
   advection test on Cartesian grid.  
     
 \item \texttt{advect\_yz} Two-dimensional (vertical plane) passive  
   advection test on Cartesian grid.  
     
 \item \texttt{carbon} Simple passive tracer experiment. Includes  
   derivative calculation. Described in detail in section  
   \ref{sect:eg-carbon-ad}.  
   
 \item \texttt{flt\_example} Example of using float package.  
     
 \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux  
   boundary conditions and poles.  
   
 \item \texttt{global\_ocean\_pressure} Global circulation in pressure  
   coordinate (non-Boussinesq ocean model). Described in detail in  
   section \ref{sect:eg-globalpressure}.  
     
 \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube  
   sphere grid.  
   
 \end{enumerate}  
   
 \subsection{Directory structure of model examples}  
   
 Each example directory has the following subdirectories:  
   
 \begin{itemize}  
 \item \texttt{code}: contains the code particular to the example. At a  
   minimum, this directory includes the following files:  
   
   \begin{itemize}  
   \item \texttt{code/packages.conf}: declares the list of packages or  
     package groups to be used.  If not included, the default version  
     is located in \texttt{pkg/pkg\_default}.  Package groups are  
     simply convenient collections of commonly used packages which are  
     defined in \texttt{pkg/pkg\_default}.  Some packages may require  
     other packages or may require their absence (that is, they are  
     incompatible) and these package dependencies are listed in  
     \texttt{pkg/pkg\_depend}.  
   
   \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to  
     the ``execution environment'' part of the code. The default  
     version is located in \texttt{eesupp/inc}.  
     
   \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to  
     the ``numerical model'' part of the code. The default version is  
     located in \texttt{model/inc}.  
     
   \item \texttt{code/SIZE.h}: declares size of underlying  
     computational grid.  The default version is located in  
     \texttt{model/inc}.  
   \end{itemize}  
     
   In addition, other include files and subroutines might be present in  
   \texttt{code} depending on the particular experiment. See Section 2  
   for more details.  
     
 \item \texttt{input}: contains the input data files required to run  
   the example. At a minimum, the \texttt{input} directory contains the  
   following files:  
   
   \begin{itemize}  
   \item \texttt{input/data}: this file, written as a namelist,  
     specifies the main parameters for the experiment.  
     
   \item \texttt{input/data.pkg}: contains parameters relative to the  
     packages used in the experiment.  
     
   \item \texttt{input/eedata}: this file contains ``execution  
     environment'' data. At present, this consists of a specification  
     of the number of threads to use in $X$ and $Y$ under multithreaded  
     execution.  
   \end{itemize}  
     
   In addition, you will also find in this directory the forcing and  
   topography files as well as the files describing the initial state  
   of the experiment.  This varies from experiment to experiment. See  
   section 2 for more details.  
   
 \item \texttt{results}: this directory contains the output file  
   \texttt{output.txt} produced by the simulation example. This file is  
   useful for comparison with your own output when you run the  
   experiment.  
 \end{itemize}  
   
 Once you have chosen the example you want to run, you are ready to  
 compile the code.  
   
337  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
338  \label{sect:buildingCode}  \label{sect:buildingCode}
339  \begin{rawhtml}  \begin{rawhtml}
# Line 550  Through the MITgcm-support list, the MIT Line 377  Through the MITgcm-support list, the MIT
377  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
378  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
379  architectures) to the  architectures) to the
380  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
381  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
382  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
383  list.  list.
# Line 604  and then calling the executable with: Line 431  and then calling the executable with:
431  where we are re-directing the stream of text output to the file  where we are re-directing the stream of text output to the file
432  \texttt{output.txt}.  \texttt{output.txt}.
433    
434    \subsection{Building/compiling the code elsewhere}
435    
436    In the example above (section \ref{sect:buildingCode}) we built the
437    executable in the {\em input} directory of the experiment for
438    convenience. You can also configure and compile the code in other
439    locations, for example on a scratch disk with out having to copy the
440    entire source tree. The only requirement to do so is you have {\tt
441      genmake2} in your path or you know the absolute path to {\tt
442      genmake2}.
443    
444    The following sections outline some possible methods of organizing
445    your source and data.
446    
447    \subsubsection{Building from the {\em ../code directory}}
448    
449    This is just as simple as building in the {\em input/} directory:
450    \begin{verbatim}
451    % cd verification/exp2/code
452    % ../../../tools/genmake2
453    % make depend
454    % make
455    \end{verbatim}
456    However, to run the model the executable ({\em mitgcmuv}) and input
457    files must be in the same place. If you only have one calculation to make:
458    \begin{verbatim}
459    % cd ../input
460    % cp ../code/mitgcmuv ./
461    % ./mitgcmuv > output.txt
462    \end{verbatim}
463    or if you will be making multiple runs with the same executable:
464    \begin{verbatim}
465    % cd ../
466    % cp -r input run1
467    % cp code/mitgcmuv run1
468    % cd run1
469    % ./mitgcmuv > output.txt
470    \end{verbatim}
471    
472    \subsubsection{Building from a new directory}
473    
474    Since the {\em input} directory contains input files it is often more
475    useful to keep {\em input} pristine and build in a new directory
476    within {\em verification/exp2/}:
477    \begin{verbatim}
478    % cd verification/exp2
479    % mkdir build
480    % cd build
481    % ../../../tools/genmake2 -mods=../code
482    % make depend
483    % make
484    \end{verbatim}
485    This builds the code exactly as before but this time you need to copy
486    either the executable or the input files or both in order to run the
487    model. For example,
488    \begin{verbatim}
489    % cp ../input/* ./
490    % ./mitgcmuv > output.txt
491    \end{verbatim}
492    or if you tend to make multiple runs with the same executable then
493    running in a new directory each time might be more appropriate:
494    \begin{verbatim}
495    % cd ../
496    % mkdir run1
497    % cp build/mitgcmuv run1/
498    % cp input/* run1/
499    % cd run1
500    % ./mitgcmuv > output.txt
501    \end{verbatim}
502    
503    \subsubsection{Building on a scratch disk}
504    
505    Model object files and output data can use up large amounts of disk
506    space so it is often the case that you will be operating on a large
507    scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
508    following commands will build the model in {\em /scratch/exp2-run1}:
509    \begin{verbatim}
510    % cd /scratch/exp2-run1
511    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
512      -mods=~/MITgcm/verification/exp2/code
513    % make depend
514    % make
515    \end{verbatim}
516    To run the model here, you'll need the input files:
517    \begin{verbatim}
518    % cp ~/MITgcm/verification/exp2/input/* ./
519    % ./mitgcmuv > output.txt
520    \end{verbatim}
521    
522    As before, you could build in one directory and make multiple runs of
523    the one experiment:
524    \begin{verbatim}
525    % cd /scratch/exp2
526    % mkdir build
527    % cd build
528    % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
529      -mods=~/MITgcm/verification/exp2/code
530    % make depend
531    % make
532    % cd ../
533    % cp -r ~/MITgcm/verification/exp2/input run2
534    % cd run2
535    % ./mitgcmuv > output.txt
536    \end{verbatim}
537    
538    
539    \subsection{Using \texttt{genmake2}}
540    \label{sect:genmake}
541    
542    To compile the code, first use the program \texttt{genmake2} (located
543    in the \texttt{tools} directory) to generate a Makefile.
544    \texttt{genmake2} is a shell script written to work with all
545    ``sh''--compatible shells including bash v1, bash v2, and Bourne.
546    Internally, \texttt{genmake2} determines the locations of needed
547    files, the compiler, compiler options, libraries, and Unix tools.  It
548    relies upon a number of ``optfiles'' located in the
549    \texttt{tools/build\_options} directory.
550    
551    The purpose of the optfiles is to provide all the compilation options
552    for particular ``platforms'' (where ``platform'' roughly means the
553    combination of the hardware and the compiler) and code configurations.
554    Given the combinations of possible compilers and library dependencies
555    ({\it eg.}  MPI and NetCDF) there may be numerous optfiles available
556    for a single machine.  The naming scheme for the majority of the
557    optfiles shipped with the code is
558    \begin{center}
559      {\bf OS\_HARDWARE\_COMPILER }
560    \end{center}
561    where
562    \begin{description}
563    \item[OS] is the name of the operating system (generally the
564      lower-case output of the {\tt 'uname'} command)
565    \item[HARDWARE] is a string that describes the CPU type and
566      corresponds to output from the  {\tt 'uname -m'} command:
567      \begin{description}
568      \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
569        and athlon
570      \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
571      \item[amd64] is AMD x86\_64 systems
572      \item[ppc] is for Mac PowerPC systems
573      \end{description}
574    \item[COMPILER] is the compiler name (generally, the name of the
575      FORTRAN executable)
576    \end{description}
577    
578    In many cases, the default optfiles are sufficient and will result in
579    usable Makefiles.  However, for some machines or code configurations,
580    new ``optfiles'' must be written. To create a new optfile, it is
581    generally best to start with one of the defaults and modify it to suit
582    your needs.  Like \texttt{genmake2}, the optfiles are all written
583    using a simple ``sh''--compatible syntax.  While nearly all variables
584    used within \texttt{genmake2} may be specified in the optfiles, the
585    critical ones that should be defined are:
586    
587    \begin{description}
588    \item[FC] the FORTRAN compiler (executable) to use
589    \item[DEFINES] the command-line DEFINE options passed to the compiler
590    \item[CPP] the C pre-processor to use
591    \item[NOOPTFLAGS] options flags for special files that should not be
592      optimized
593    \end{description}
594    
595    For example, the optfile for a typical Red Hat Linux machine (``ia32''
596    architecture) using the GCC (g77) compiler is
597    \begin{verbatim}
598    FC=g77
599    DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
600    CPP='cpp  -traditional -P'
601    NOOPTFLAGS='-O0'
602    #  For IEEE, use the "-ffloat-store" option
603    if test "x$IEEE" = x ; then
604        FFLAGS='-Wimplicit -Wunused -Wuninitialized'
605        FOPTIM='-O3 -malign-double -funroll-loops'
606    else
607        FFLAGS='-Wimplicit -Wunused -ffloat-store'
608        FOPTIM='-O0 -malign-double'
609    fi
610    \end{verbatim}
611    
612    If you write an optfile for an unrepresented machine or compiler, you
613    are strongly encouraged to submit the optfile to the MITgcm project
614    for inclusion.  Please send the file to the
615    \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
616    \begin{center}
617      MITgcm-support@mitgcm.org
618    \end{center}
619    \begin{rawhtml} </A> \end{rawhtml}
620    mailing list.
621    
622    In addition to the optfiles, \texttt{genmake2} supports a number of
623    helpful command-line options.  A complete list of these options can be
624    obtained from:
625    \begin{verbatim}
626    % genmake2 -h
627    \end{verbatim}
628    
629    The most important command-line options are:
630    \begin{description}
631      
632    \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
633      should be used for a particular build.
634      
635      If no "optfile" is specified (either through the command line or the
636      MITGCM\_OPTFILE environment variable), genmake2 will try to make a
637      reasonable guess from the list provided in {\em
638        tools/build\_options}.  The method used for making this guess is
639      to first determine the combination of operating system and hardware
640      (eg. "linux\_ia32") and then find a working FORTRAN compiler within
641      the user's path.  When these three items have been identified,
642      genmake2 will try to find an optfile that has a matching name.
643      
644    \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
645      set of packages to be used.  The normal order of precedence for
646      packages is as follows:
647      \begin{enumerate}
648      \item If available, the command line (\texttt{--pdefault}) settings
649        over-rule any others.
650    
651      \item Next, \texttt{genmake2} will look for a file named
652        ``\texttt{packages.conf}'' in the local directory or in any of the
653        directories specified with the \texttt{--mods} option.
654        
655      \item Finally, if neither of the above are available,
656        \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
657      \end{enumerate}
658      
659    \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
660      used for packages.
661      
662      If not specified, the default dependency file {\em pkg/pkg\_depend}
663      is used.  The syntax for this file is parsed on a line-by-line basis
664      where each line containes either a comment ("\#") or a simple
665      "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol
666      specifies a "must be used with" or a "must not be used with"
667      relationship, respectively.  If no rule is specified, then it is
668      assumed that the two packages are compatible and will function
669      either with or without each other.
670      
671    \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
672      automatic differentiation options file to be used.  The file is
673      analogous to the ``optfile'' defined above but it specifies
674      information for the AD build process.
675      
676      The default file is located in {\em
677        tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
678      and "TAMC" compilers.  An alternate version is also available at
679      {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
680      "STAF" compiler.  As with any compilers, it is helpful to have their
681      directories listed in your {\tt \$PATH} environment variable.
682      
683    \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
684      directories containing ``modifications''.  These directories contain
685      files with names that may (or may not) exist in the main MITgcm
686      source tree but will be overridden by any identically-named sources
687      within the ``MODS'' directories.
688      
689      The order of precedence for this "name-hiding" is as follows:
690      \begin{itemize}
691      \item ``MODS'' directories (in the order given)
692      \item Packages either explicitly specified or provided by default
693        (in the order given)
694      \item Packages included due to package dependencies (in the order
695        that that package dependencies are parsed)
696      \item The "standard dirs" (which may have been specified by the
697        ``-standarddirs'' option)
698      \end{itemize}
699      
700    \item[\texttt{--mpi}] This option enables certain MPI features (using
701      CPP \texttt{\#define}s) within the code and is necessary for MPI
702      builds (see Section \ref{sect:mpi-build}).
703      
704    \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
705      soft-links and other bugs common with the \texttt{make} versions
706      provided by commercial Unix vendors, GNU \texttt{make} (sometimes
707      called \texttt{gmake}) should be preferred.  This option provides a
708      means for specifying the make executable to be used.
709      
710    \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
711      machines, the ``bash'' shell is unavailable.  To run on these
712      systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
713      a Bourne, POSIX, or compatible) shell.  The syntax in these
714      circumstances is:
715      \begin{center}
716        \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
717      \end{center}
718      where \texttt{/bin/sh} can be replaced with the full path and name
719      of the desired shell.
720    
721    \end{description}
722    
723    
724    \subsection{Building with MPI}
725    \label{sect:mpi-build}
726    
727    Building MITgcm to use MPI libraries can be complicated due to the
728    variety of different MPI implementations available, their dependencies
729    or interactions with different compilers, and their often ad-hoc
730    locations within file systems.  For these reasons, its generally a
731    good idea to start by finding and reading the documentation for your
732    machine(s) and, if necessary, seeking help from your local systems
733    administrator.
734    
735    The steps for building MITgcm with MPI support are:
736    \begin{enumerate}
737      
738    \item Determine the locations of your MPI-enabled compiler and/or MPI
739      libraries and put them into an options file as described in Section
740      \ref{sect:genmake}.  One can start with one of the examples in:
741      \begin{rawhtml} <A
742        href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">
743      \end{rawhtml}
744      \begin{center}
745        \texttt{MITgcm/tools/build\_options/}
746      \end{center}
747      \begin{rawhtml} </A> \end{rawhtml}
748      such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
749      \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
750      hand.  You may need help from your user guide or local systems
751      administrator to determine the exact location of the MPI libraries.
752      If libraries are not installed, MPI implementations and related
753      tools are available including:
754      \begin{itemize}
755      \item \begin{rawhtml} <A
756          href="http://www-unix.mcs.anl.gov/mpi/mpich/">
757        \end{rawhtml}
758        MPICH
759        \begin{rawhtml} </A> \end{rawhtml}
760    
761      \item \begin{rawhtml} <A
762          href="http://www.lam-mpi.org/">
763        \end{rawhtml}
764        LAM/MPI
765        \begin{rawhtml} </A> \end{rawhtml}
766    
767      \item \begin{rawhtml} <A
768          href="http://www.osc.edu/~pw/mpiexec/">
769        \end{rawhtml}
770        MPIexec
771        \begin{rawhtml} </A> \end{rawhtml}
772      \end{itemize}
773      
774    \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
775      (see Section \ref{sect:genmake}) using commands such as:
776    {\footnotesize \begin{verbatim}
777      %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
778      %  make depend
779      %  make
780    \end{verbatim} }
781      
782    \item Run the code with the appropriate MPI ``run'' or ``exec''
783      program provided with your particular implementation of MPI.
784      Typical MPI packages such as MPICH will use something like:
785    \begin{verbatim}
786      %  mpirun -np 4 -machinefile mf ./mitgcmuv
787    \end{verbatim}
788      Sightly more complicated scripts may be needed for many machines
789      since execution of the code may be controlled by both the MPI
790      library and a job scheduling and queueing system such as PBS,
791      LoadLeveller, Condor, or any of a number of similar tools.  A few
792      example scripts (those used for our \begin{rawhtml} <A
793        href="http://mitgcm.org/testing.html"> \end{rawhtml}regular
794      verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
795      at:
796      \begin{rawhtml} <A
797        href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
798      \end{rawhtml}
799      {\footnotesize \tt
800        http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }
801      \begin{rawhtml} </A> \end{rawhtml}
802    
803    \end{enumerate}
804    
805    An example of the above process on the MITgcm cluster (``cg01'') using
806    the GNU g77 compiler and the mpich MPI library is:
807    
808    {\footnotesize \begin{verbatim}
809      %  cd MITgcm/verification/exp5
810      %  mkdir build
811      %  cd build
812      %  ../../../tools/genmake2 -mpi -mods=../code \
813           -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
814      %  make depend
815      %  make
816      %  cd ../input
817      %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
818           -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
819    \end{verbatim} }
820    
821  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
822  \label{sect:runModel}  \label{sect:runModel}
# Line 658  package.  At a minimum, the instantaneou Line 871  package.  At a minimum, the instantaneou
871  written out, which is made of the following files:  written out, which is made of the following files:
872    
873  \begin{itemize}  \begin{itemize}
874  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
875  0 $ eastward).    and positive eastward).
876    
877  \item \texttt{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
878  and $> 0$ northward).    (m/s and positive northward).
879    
880  \item \texttt{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
881  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
882  i.e. downward).    towards increasing pressure i.e. downward).
883    
884  \item \texttt{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
885  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
886    
887  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
888  (g/kg).    vapor (g/kg).
889    
890  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
891  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
892  \end{itemize}  \end{itemize}
893    
894  The chain \texttt{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
895  iteration number at which the output is written out. For example, \texttt{%  iteration number at which the output is written out. For example,
896  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
897    
898  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
899    
# Line 717  format and can thus be browsed and/or pl Line 930  format and can thus be browsed and/or pl
930    with every netCDF install:    with every netCDF install:
931    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
932  \begin{verbatim}  \begin{verbatim}
933       http://www.unidata.ucar.edu/packages/netcdf/  http://www.unidata.ucar.edu/packages/netcdf/
934  \end{verbatim}  \end{verbatim}
935    \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF    \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
936    binaries into formatted ASCII text files.    binaries into formatted ASCII text files.
# Line 726  format and can thus be browsed and/or pl Line 939  format and can thus be browsed and/or pl
939    to plot netCDF data and it runs on most OSes:    to plot netCDF data and it runs on most OSes:
940    \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}    \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
941  \begin{verbatim}  \begin{verbatim}
942       http://meteora.ucsd.edu/~pierce/ncview_home_page.html  http://meteora.ucsd.edu/~pierce/ncview_home_page.html
943  \end{verbatim}  \end{verbatim}
944    \begin{rawhtml} </A> \end{rawhtml}    \begin{rawhtml} </A> \end{rawhtml}
945        
946  \item MatLAB(c) and other common post-processing environments provide  \item MatLAB(c) and other common post-processing environments provide
947    various netCDF interfaces including:    various netCDF interfaces including:
948      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
949    \begin{verbatim}
950    http://mexcdf.sourceforge.net/
951    \end{verbatim}
952      \begin{rawhtml} </A> \end{rawhtml}
953    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
954  \begin{verbatim}  \begin{verbatim}
955  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
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