/[MITgcm]/manual/s_getstarted/text/getting_started.tex

Diff of /manual/s_getstarted/text/getting_started.tex

Parent Directory | Revision Log | View Revision Graph Revision Graph | View Patch Patch

-revision 1.15 by edhill,
Wed Jan 28 20:50:14 2004 UTC
+revision 1.17 by edhill,
Thu Jan 29 15:11:39 2004 UTC
 Line 39 
 http://mitgcm.org/pipermail/mitgcm-suppo
  \begin{rawhtml} </A> \end{rawhtml}
  Essentially all of the MITgcm web pages can be searched using a
  popular web crawler such as Google or through our own search facility:
+ \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}
  \begin{verbatim}
  http://mitgcm.org/htdig/
  \end{verbatim}
-Line 108 
 To obtain the latest sources type:
+Line 109 
 To obtain the latest sources type:
  \end{verbatim}
  or to get a specific release type:
  \begin{verbatim}
- % cvs co -d directory -P -r release1_beta1 MITgcm
+ % cvs co -P -r checkpoint52i_post  MITgcm
  \end{verbatim}
  The MITgcm web site contains further directions concerning the source
  code and CVS.  It also contains a web interface to our CVS archive so
  that one may easily view the state of files, revisions, and other
  development milestones:
- \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
+ \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}
  \begin{verbatim}
  http://mitgcm.org/source_code.html
  \end{verbatim}
-Line 129 
 track of your file versions with respect
+Line 130 
 track of your file versions with respect
  the files in \textit{CVS}!  You can also use CVS to download code
  updates.  More extensive information on using CVS for maintaining
  MITgcm code can be found
- \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}
  here
  \begin{rawhtml} </A> \end{rawhtml}
  .
-Line 149 
 The tar file still contains CVS informat
+Line 150 
 The tar file still contains CVS informat
  delete; even if you do not use CVS yourself the information can help
  us if you should need to send us your copy of the code.  If a recent
  tar file does not exist, then please contact the developers through
- the MITgcm-support list.
+ the
+ \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
+ MITgcm-support@mitgcm.org
+ \begin{rawhtml} </A> \end{rawhtml}
+ mailing list.
  \paragraph*{Upgrading from an earlier version}
-Line 161 
 your copy instead of downloading the ent
+Line 166 
 your copy instead of downloading the ent
  \end{verbatim}
  and then issue the cvs update command such as:
  \begin{verbatim}
- % cvs -q update -r release1_beta1 -d -P
+ % cvs -q update -r checkpoint52i_post -d -P
  \end{verbatim}
- This will update the ``tag'' to ``release1\_beta1'', add any new
+ This will update the ``tag'' to ``checkpoint52i\_post'', add any new
  directories (-d) and remove any empty directories (-P). The -q option
  means be quiet which will reduce the number of messages you'll see in
  the terminal. If you have modified the code prior to upgrading, CVS
-Line 177 
 If the list of conflicts scrolled off th
+Line 182 
 If the list of conflicts scrolled off th
  cvs update command and it will report the conflicts. Conflicts are
  indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and
  ``$>>>>>>>$''. For example,
+ {\small
  \begin{verbatim}
  <<<<<<< ini_parms.F
       & bottomDragLinear,myOwnBottomDragCoefficient,
-Line 184 
 indicated in the code by the delimites `
+Line 190 
 indicated in the code by the delimites `
       & bottomDragLinear,bottomDragQuadratic,
  >>>>>>> 1.18
  \end{verbatim}
+ }
  means that you added ``myOwnBottomDragCoefficient'' to a namelist at
  the same time and place that we added ``bottomDragQuadratic''. You
  need to resolve this conflict and in this case the line should be
  changed to:
+ {\small
  \begin{verbatim}
       & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
  \end{verbatim}
+ }
  and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted.
  Unless you are making modifications which exactly parallel
  developments we make, these types of conflicts should be rare.
-Line 224 
 model code. The execution environment su
+Line 233 
 model code. The execution environment su
  \textit{eesupp} directory. The grid point model code is held under the
  \textit{model} directory. Code execution actually starts in the
  \textit{eesupp} routines and not in the \textit{model} routines. For
- this reason the top-level
+ this reason the top-level \textit{MAIN.F} is in the
- \textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,
+ \textit{eesupp/src} directory. In general, end-users should not need
- end-users should not need to worry about this level. The top-level routine
+ to worry about this level. The top-level routine for the numerical
- for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%
+ part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is
- }. Here is a brief description of the directory structure of the model under
+ a brief description of the directory structure of the model under the
- the root tree (a detailed description is given in section 3: Code structure).
+ root tree (a detailed description is given in section 3: Code
+ structure).
  \begin{itemize}
- \item \textit{bin}: this directory is initially empty. It is the default
- directory in which to compile the code.
+ \item \textit{bin}: this directory is initially empty. It is the
+   default directory in which to compile the code.
  \item \textit{diags}: contains the code relative to time-averaged
- diagnostics. It is subdivided into two subdirectories \textit{inc} and
+   diagnostics. It is subdivided into two subdirectories \textit{inc}
- \textit{src} that contain include files (*.\textit{h} files) and Fortran
+   and \textit{src} that contain include files (*.\textit{h} files) and
- subroutines (*.\textit{F} files), respectively.
+   Fortran subroutines (*.\textit{F} files), respectively.
  \item \textit{doc}: contains brief documentation notes.
- \item \textit{eesupp}: contains the execution environment source code. Also
+ \item \textit{eesupp}: contains the execution environment source code.
- subdivided into two subdirectories \textit{inc} and \textit{src}.
+   Also subdivided into two subdirectories \textit{inc} and
+   \textit{src}.
- \item \textit{exe}: this directory is initially empty. It is the default
- directory in which to execute the code.
+ \item \textit{exe}: this directory is initially empty. It is the
+   default directory in which to execute the code.
- \item \textit{model}: this directory contains the main source code. Also
- subdivided into two subdirectories \textit{inc} and \textit{src}.
+ \item \textit{model}: this directory contains the main source code.
+   Also subdivided into two subdirectories \textit{inc} and
- \item \textit{pkg}: contains the source code for the packages. Each package
+   \textit{src}.
- corresponds to a subdirectory. For example, \textit{gmredi} contains the
- code related to the Gent-McWilliams/Redi scheme, \textit{aim} the code
+ \item \textit{pkg}: contains the source code for the packages. Each
- relative to the atmospheric intermediate physics. The packages are described
+   package corresponds to a subdirectory. For example, \textit{gmredi}
- in detail in section 3.
+   contains the code related to the Gent-McWilliams/Redi scheme,
+   \textit{aim} the code relative to the atmospheric intermediate
- \item \textit{tools}: this directory contains various useful tools. For
+   physics. The packages are described in detail in section 3.
- example, \textit{genmake2} is a script written in csh (C-shell) that should
- be used to generate your makefile. The directory \textit{adjoint} contains
+ \item \textit{tools}: this directory contains various useful tools.
- the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that
+   For example, \textit{genmake2} is a script written in csh (C-shell)
- generates the adjoint code. The latter is described in details in part V.
+   that should be used to generate your makefile. The directory
+   \textit{adjoint} contains the makefile specific to the Tangent
+   linear and Adjoint Compiler (TAMC) that generates the adjoint code.
+   The latter is described in details in part V.
  \item \textit{utils}: this directory contains various utilities. The
- subdirectory \textit{knudsen2} contains code and a makefile that
+   subdirectory \textit{knudsen2} contains code and a makefile that
- compute coefficients of the polynomial approximation to the knudsen
+   compute coefficients of the polynomial approximation to the knudsen
- formula for an ocean nonlinear equation of state. The \textit{matlab}
+   formula for an ocean nonlinear equation of state. The
- subdirectory contains matlab scripts for reading model output directly
+   \textit{matlab} subdirectory contains matlab scripts for reading
- into matlab. \textit{scripts} contains C-shell post-processing
+   model output directly into matlab. \textit{scripts} contains C-shell
- scripts for joining processor-based and tiled-based model output.
+   post-processing scripts for joining processor-based and tiled-based
+   model output.
+ \item \textit{verification}: this directory contains the model
+   examples. See section \ref{sect:modelExamples}.
- \item \textit{verification}: this directory contains the model examples. See
- section \ref{sect:modelExamples}.
  \end{itemize}
  \section{Example experiments}
-Line 294 
 below.
+Line 310 
 below.
  \subsection{Full list of model examples}
  \begin{enumerate}
  \item \textit{exp0} - single layer, ocean double gyre (barotropic with
    free-surface). This experiment is described in detail in section
    \ref{sect:eg-baro}.
-Line 383 
 Each example directory has the following
+Line 400 
 Each example directory has the following
  \begin{itemize}
  \item \textit{code}: contains the code particular to the example. At a
- minimum, this directory includes the following files:
+   minimum, this directory includes the following files:
- \begin{itemize}
+   \begin{itemize}
- \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
+   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
-   the ``execution environment'' part of the code. The default version
+     the ``execution environment'' part of the code. The default
-   is located in \textit{eesupp/inc}.
+     version is located in \textit{eesupp/inc}.
- \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the
+   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
-   ``numerical model'' part of the code. The default version is located
+     the ``numerical model'' part of the code. The default version is
-   in \textit{model/inc}.
+     located in \textit{model/inc}.
+   \item \textit{code/SIZE.h}: declares size of underlying
+     computational grid.  The default version is located in
+     \textit{model/inc}.
+   \end{itemize}
+   In addition, other include files and subroutines might be present in
+   \textit{code} depending on the particular experiment. See Section 2
+   for more details.
- \item \textit{code/SIZE.h}: declares size of underlying computational
-   grid.  The default version is located in \textit{model/inc}.
- \end{itemize}
- In addition, other include files and subroutines might be present in
- \textit{code} depending on the particular experiment. See Section 2
- for more details.
  \item \textit{input}: contains the input data files required to run
    the example. At a minimum, the \textit{input} directory contains the
    following files:
- \begin{itemize}
+   \begin{itemize}
- \item \textit{input/data}: this file, written as a namelist, specifies
+   \item \textit{input/data}: this file, written as a namelist,
-   the main parameters for the experiment.
+     specifies the main parameters for the experiment.
- \item \textit{input/data.pkg}: contains parameters relative to the
+   \item \textit{input/data.pkg}: contains parameters relative to the
-   packages used in the experiment.
+     packages used in the experiment.
- \item \textit{input/eedata}: this file contains ``execution
+   \item \textit{input/eedata}: this file contains ``execution
-   environment'' data. At present, this consists of a specification of
+     environment'' data. At present, this consists of a specification
-   the number of threads to use in $X$ and $Y$ under multithreaded
+     of the number of threads to use in $X$ and $Y$ under multithreaded
-   execution.
+     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 \textit{results}: this directory contains the output file
+   \textit{output.txt} produced by the simulation example. This file is
+   useful for comparison with your own output when you run the
+   experiment.
  \end{itemize}
- In addition, you will also find in this directory the forcing and topography
+ Once you have chosen the example you want to run, you are ready to
- files as well as the files describing the initial state of the experiment.
+ compile the code.
- This varies from experiment to experiment. See section 2 for more details.
- \item \textit{results}: this directory contains the output file \textit{%
- 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.
  \section{Building the code}
  \label{sect:buildingCode}
-Line 437 
 the code.
+Line 457 
 the code.
  To compile the code, we use the {\em make} program. This uses a file
  ({\em Makefile}) that allows us to pre-process source files, specify
  compiler and optimization options and also figures out any file
- dependencies. We supply a script ({\em genmake}), described in section
+ dependencies. We supply a script ({\em genmake2}), described in
- \ref{sect:genmake}, that automatically creates the {\em Makefile} for
+ section \ref{sect:genmake}, that automatically creates the {\em
- you. You then need to build the dependencies and compile the code.
+   Makefile} for you. You then need to build the dependencies and
+ compile the code.
  As an example, let's assume that you want to build and run experiment
- \textit{verification/exp2}. The are multiple ways and places to actually
+ \textit{verification/exp2}. The are multiple ways and places to
- do this but here let's build the code in
+ actually do this but here let's build the code in
  \textit{verification/exp2/input}:
  \begin{verbatim}
  % cd verification/exp2/input
  \end{verbatim}
  First, build the {\em Makefile}:
  \begin{verbatim}
- % ../../../tools/genmake -mods=../code
+ % ../../../tools/genmake2 -mods=../code
  \end{verbatim}
  The command line option tells {\em genmake} to override model source
  code with any files in the directory {\em ./code/}.
- If there is no \textit{.genmakerc} in the \textit{input} directory, you have
+ On many systems, the {\em genmake2} program will be able to
- to use the following options when invoking \textit{genmake}:
+ automatically recognize the hardware, find compilers and other tools
+ within the user's path (``echo \$PATH''), and then choose an
+ appropriate set of options from the files contained in the {\em
+   tools/build\_options} directory.  Under some circumstances, a user
+ may have to create a new ``optfile'' in order to specify the exact
+ combination of compiler, compiler flags, libraries, and other options
+ necessary to build a particular configuration of MITgcm.  In such
+ cases, it is generally helpful to read the existing ``optfiles'' and
+ mimic their syntax.
+ Through the MITgcm-support list, the MITgcm developers are willing to
+ provide help writing or modifing ``optfiles''.  And we encourage users
+ to post new ``optfiles'' (particularly ones for new machines or
+ architectures) to the
+ \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
+ MITgcm-support@mitgcm.org
+ \begin{rawhtml} </A> \end{rawhtml}
+ list.
+ To specify an optfile to {\em genmake2}, the syntax is:
  \begin{verbatim}
- % ../../../tools/genmake  -mods=../code
+ % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
  \end{verbatim}
- Next, create the dependencies:
+ Once a {\em Makefile} has been generated, we create the dependencies:
  \begin{verbatim}
  % make depend
  \end{verbatim}
- This modifies {\em Makefile} by attaching a [long] list of files on
+ This modifies the {\em Makefile} by attaching a [long] list of files
- which other files depend. The purpose of this is to reduce
+ upon which other files depend. The purpose of this is to reduce
- re-compilation if and when you start to modify the code. {\tt make
+ re-compilation if and when you start to modify the code. The {\tt make
- depend} also created links from the model source to this directory.
+   depend} command also creates links from the model source to this
+ directory.
- Now compile the code:
+ Next compile the code:
  \begin{verbatim}
  % make
  \end{verbatim}
  The {\tt make} command creates an executable called \textit{mitgcmuv}.
+ Additional make ``targets'' are defined within the makefile to aid in
+ the production of adjoint and other versions of MITgcm.
  Now you are ready to run the model. General instructions for doing so are
  given in section \ref{sect:runModel}. Here, we can run the model with:
-Line 492 
 executable in the {\em input} directory
+Line 535 
 executable in the {\em input} directory
  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
- genmake} in your path or you know the absolute path to {\tt genmake}.
+   genmake2} in your path or you know the absolute path to {\tt
+   genmake2}.
- The following sections outline some possible methods of organizing you
+ The following sections outline some possible methods of organizing
- source and data.
+ 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/genmake
+ % ../../../tools/genmake2
  % make depend
  % make
  \end{verbatim}
-Line 531 
 within {\em verification/exp2/}:
+Line 575 
 within {\em verification/exp2/}:
  % cd verification/exp2
  % mkdir build
  % cd build
- % ../../../tools/genmake -mods=../code
+ % ../../../tools/genmake2 -mods=../code
  % make depend
  % make
  \end{verbatim}
-Line 553 
 running in a new directory each time mig
+Line 597 
 running in a new directory each time mig
  % ./mitgcmuv > output.txt
  \end{verbatim}
- \subsubsection{Building from on a scratch disk}
+ \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
-Line 561 
 scratch disk. Assuming the model source
+Line 605 
 scratch disk. Assuming the model source
  following commands will build the model in {\em /scratch/exp2-run1}:
  \begin{verbatim}
  % cd /scratch/exp2-run1
- % ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
+ % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
+   -mods=~/MITgcm/verification/exp2/code
  % make depend
  % make
  \end{verbatim}
-Line 577 
 the one experiment:
+Line 622 
 the one experiment:
  % cd /scratch/exp2
  % mkdir build
  % cd build
- % ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
+ % ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
+   -mods=~/MITgcm/verification/exp2/code
  % make depend
  % make
  % cd ../
-Line 588 
 the one experiment:
+Line 634 
 the one experiment:
- \subsection{\textit{genmake}}
+ \subsection{Using \textit{genmake2}}
  \label{sect:genmake}
- To compile the code, use the script \textit{genmake} located in the \textit{%
+ To compile the code, first use the program \texttt{genmake2} (located
- tools} directory. \textit{genmake} is a script that generates the makefile.
+ in the \textit{tools} directory) to generate a Makefile.
- It has been written so that the code can be compiled on a wide diversity of
+ \texttt{genmake2} is a shell script written to work with all
- machines and systems. However, if it doesn't work the first time on your
+ ``sh''--compatible shells including bash v1, bash v2, and Bourne.
- platform, you might need to edit certain lines of \textit{genmake} in the
+ Internally, \texttt{genmake2} determines the locations of needed
- section containing the setups for the different machines. The file is
+ files, the compiler, compiler options, libraries, and Unix tools.  It
- structured like this:
+ relies upon a number of ``optfiles'' located in the {\em
- \begin{verbatim}
+   tools/build\_options} directory.
-         .
-         .
+ The purpose of the optfiles is to provide all the compilation options
-         .
+ for particular ``platforms'' (where ``platform'' roughly means the
- general instructions (machine independent)
+ 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
-     - setup machine 1
+ optfiles shipped with the code is
-     - setup machine 2
+ \begin{center}
-     - setup machine 3
+   {\bf OS\_HARDWARE\_COMPILER }
-     - setup machine 4
+ \end{center}
-        etc
+ where
-         .
+ \begin{description}
-         .
+ \item[OS] is the name of the operating system (generally the
-         .
+   lower-case output of the {\tt 'uname'} command)
- \end{verbatim}
+ \item[HARDWARE] is a string that describes the CPU type and
+   corresponds to output from the  {\tt 'uname -m'} command:
- For example, the setup corresponding to a DEC alpha machine is reproduced
+   \begin{description}
- here:
+   \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
- \begin{verbatim}
+     and athlon
-   case OSF1+mpi:
+   \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
-     echo "Configuring for DEC Alpha"
+   \item[amd64] is AMD x86\_64 systems
-     set CPP        = ( '/usr/bin/cpp -P' )
+   \item[ppc] is for Mac PowerPC systems
-     set DEFINES    = ( ${DEFINES}  '-DTARGET_DEC -DWORDLENGTH=1' )
+   \end{description}
-     set KPP        = ( 'kapf' )
+ \item[COMPILER] is the compiler name (generally, the name of the
-     set KPPFILES   = ( 'main.F' )
+   FORTRAN executable)
-     set KFLAGS1    = ( '-scan=132 -noconc -cmp=' )
+ \end{description}
-     set FC         = ( 'f77' )
-     set FFLAGS     = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' )
-     set FOPTIM     = ( '-O5 -fast -tune host -inline all' )
-     set NOOPTFLAGS = ( '-O0' )
-     set LIBS       = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' )
-     set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')
-     set RMFILES    = ( '*.p.out' )
-     breaksw
- \end{verbatim}
- Typically, these are the lines that you might need to edit to make \textit{%
- genmake} work on your platform if it doesn't work the first time. \textit{%
- genmake} understands several options that are described here:
- \begin{itemize}
- \item -rootdir=dir
- indicates where the model root directory is relative to the directory where
- you are compiling. This option is not needed if you compile in the \textit{%
- bin} directory (which is the default compilation directory) or within the
- \textit{verification} tree.
- \item -mods=dir1,dir2,...
- indicates the relative or absolute paths directories where the sources
- should take precedence over the default versions (located in \textit{model},
- \textit{eesupp},...). Typically, this option is used when running the
- examples, see below.
- \item -enable=pkg1,pkg2,...
- enables packages source code \textit{pkg1}, \textit{pkg2},... when creating
- the makefile.
- \item -disable=pkg1,pkg2,...
- disables packages source code \textit{pkg1}, \textit{pkg2},... when creating
- the makefile.
- \item -platform=machine
+ 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:
- specifies the platform for which you want the makefile. In general, you
+ \begin{description}
- won't need this option. \textit{genmake} will select the right machine for
+ \item[FC] the FORTRAN compiler (executable) to use
- you (the one you're working on!). However, this option is useful if you have
+ \item[DEFINES] the command-line DEFINE options passed to the compiler
- a choice of several compilers on one machine and you want to use the one
+ \item[CPP] the C pre-processor to use
- that is not the default (ex: \texttt{pgf77} instead of \texttt{f77} under
+ \item[NOOPTFLAGS] options flags for special files that should not be
- Linux).
+   optimized
+ \end{description}
- \item -mpi
+ 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.
- this is used when you want to run the model in parallel processing mode
+ In addition to the optfiles, \texttt{genmake2} supports a number of
- under mpi (see section on parallel computation for more details).
+ helpful command-line options.  A complete list of these options can be
+ obtained from:
+ \begin{verbatim}
+ % genmake2 -h
+ \end{verbatim}
- \item -jam
+ 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{--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{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
+   set of packages to be used.
+   If not set, the default package list will be read from {\em
+     pkg/pkg\_default}
+ \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{--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.
- this is used when you want to run the model in parallel processing mode
+ \end{description}
- under jam (see section on parallel computation for more details).
- \end{itemize}
- For some of the examples, there is a file called \textit{.genmakerc} in the
- \textit{input} directory that has the relevant \textit{genmake} options for
- that particular example. In this way you don't need to type the options when
- invoking \textit{genmake}.
  \section{Running the model}
-Line 714 
 normally re-direct the {\em stdout} stre
+Line 819 
 normally re-direct the {\em stdout} stre
  % ./mitgcmuv > output.txt
  \end{verbatim}
- For the example experiments in {\em vericication}, an example of the
+ For the example experiments in {\em verification}, an example of the
  output is kept in {\em results/output.txt} for comparison. You can compare
  your {\em output.txt} with this one to check that the set-up works.
-Line 803 
 Some examples of reading and visualizing
+Line 908 
 Some examples of reading and visualizing
  \section{Doing it yourself: customizing the code}
  When you are ready to run the model in the configuration you want, the
- easiest thing is to use and adapt the setup of the case studies experiment
+ easiest thing is to use and adapt the setup of the case studies
- (described previously) that is the closest to your configuration. Then, the
+ experiment (described previously) that is the closest to your
- amount of setup will be minimized. In this section, we focus on the setup
+ configuration. Then, the amount of setup will be minimized. In this
- relative to the ''numerical model'' part of the code (the setup relative to
+ section, we focus on the setup relative to the ``numerical model''
- the ''execution environment'' part is covered in the parallel implementation
+ part of the code (the setup relative to the ``execution environment''
- section) and on the variables and parameters that you are likely to change.
+ part is covered in the parallel implementation section) and on the
+ variables and parameters that you are likely to change.
  \subsection{Configuration and setup}
- The CPP keys relative to the ''numerical model'' part of the code are all
+ The CPP keys relative to the ``numerical model'' part of the code are
- defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{%
+ all defined and set in the file \textit{CPP\_OPTIONS.h }in the
- model/inc }or in one of the \textit{code }directories of the case study
+ directory \textit{ model/inc }or in one of the \textit{code
- experiments under \textit{verification.} The model parameters are defined
+ }directories of the case study experiments under
- and declared in the file \textit{model/inc/PARAMS.h }and their default
+ \textit{verification.} The model parameters are defined and declared
- values are set in the routine \textit{model/src/set\_defaults.F. }The
+ in the file \textit{model/inc/PARAMS.h }and their default values are
- default values can be modified in the namelist file \textit{data }which
+ set in the routine \textit{model/src/set\_defaults.F. }The default
- needs to be located in the directory where you will run the model. The
+ values can be modified in the namelist file \textit{data }which needs
- parameters are initialized in the routine \textit{model/src/ini\_parms.F}.
+ to be located in the directory where you will run the model. The
- Look at this routine to see in what part of the namelist the parameters are
+ parameters are initialized in the routine
- located.
+ \textit{model/src/ini\_parms.F}.  Look at this routine to see in what
+ part of the namelist the parameters are located.
- In what follows the parameters are grouped into categories related to the
- computational domain, the equations solved in the model, and the simulation
+ In what follows the parameters are grouped into categories related to
- controls.
+ the computational domain, the equations solved in the model, and the
+ simulation controls.
  \subsection{Computational domain, geometry and time-discretization}
- \begin{itemize}
+ \begin{description}
- \item dimensions
+ \item[dimensions] \
- \end{itemize}
+   The number of points in the x, y,\textit{\ }and r\textit{\
- The number of points in the x, y,\textit{\ }and r\textit{\ }directions are
+   }directions are represented by the variables \textbf{sNx}\textit{,
- represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }%
+   }\textbf{sNy}\textit{, } and \textbf{Nr}\textit{\ }respectively
- and \textbf{Nr}\textit{\ }respectively which are declared and set in the
+   which are declared and set in the file \textit{model/inc/SIZE.h.
- file \textit{model/inc/SIZE.h. }(Again, this assumes a mono-processor
+   }(Again, this assumes a mono-processor calculation. For
- calculation. For multiprocessor calculations see section on parallel
+   multiprocessor calculations see section on parallel implementation.)
- implementation.)
+ \item[grid] \
- \begin{itemize}
- \item grid
+   Three different grids are available: cartesian, spherical polar, and
- \end{itemize}
+   curvilinear (including the cubed sphere). The grid is set through
+   the logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{
- Three different grids are available: cartesian, spherical polar, and
+     usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{
- curvilinear (including the cubed sphere). The grid is set through the
+     usingCurvilinearGrid}\textit{. }In the case of spherical and
- logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{%
+   curvilinear grids, the southern boundary is defined through the
- usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{%
+   variable \textbf{phiMin} \textit{\ }which corresponds to the
- usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear
+   latitude of the southern most cell face (in degrees). The resolution
- grids, the southern boundary is defined through the variable \textbf{phiMin}%
+   along the x and y directions is controlled by the 1D arrays
- \textit{\ }which corresponds to the latitude of the southern most cell face
+   \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters in
- (in degrees). The resolution along the x and y directions is controlled by
+   the case of a cartesian grid, in degrees otherwise). The vertical
- the 1D arrays \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters
+   grid spacing is set through the 1D array \textbf{delz }for the ocean
- in the case of a cartesian grid, in degrees otherwise). The vertical grid
+   (in meters) or \textbf{delp}\textit{\ }for the atmosphere (in Pa).
- spacing is set through the 1D array \textbf{delz }for the ocean (in meters)
+   The variable \textbf{ Ro\_SeaLevel} represents the standard position
- or \textbf{delp}\textit{\ }for the atmosphere (in Pa). The variable \textbf{%
+   of Sea-Level in ''R'' coordinate. This is typically set to 0m for
- Ro\_SeaLevel} represents the standard position of Sea-Level in ''R''
+   the ocean (default value) and 10$ ^{5}$Pa for the atmosphere. For
- coordinate. This is typically set to 0m for the ocean (default value) and 10$%
+   the atmosphere, also set the logical variable \textbf{groundAtK1} to
- ^{5}$Pa for the atmosphere. For the atmosphere, also set the logical
+   '.\texttt{TRUE}.'. which put the first level (k=1) at the lower
- variable \textbf{groundAtK1} to '.\texttt{TRUE}.'. which put the first level
+   boundary (ground).
- (k=1) at the lower boundary (ground).
+   For the cartesian grid case, the Coriolis parameter $f$ is set
- For the cartesian grid case, the Coriolis parameter $f$ is set through the
+   through the variables \textbf{f0}\textit{\ }and
- variables \textbf{f0}\textit{\ }and \textbf{beta}\textit{\ }which correspond
+   \textbf{beta}\textit{\ }which correspond to the reference Coriolis
- to the reference Coriolis parameter (in s$^{-1}$) and $\frac{\partial f}{%
+   parameter (in s$^{-1}$) and $\frac{\partial f}{ \partial y}$(in
- \partial y}$(in m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ }%
+   m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ } is set
- is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
+   to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
- southern edge of the domain.
+   southern edge of the domain.
- \begin{itemize}
+ \item[topography - full and partial cells] \
- \item topography - full and partial cells
- \end{itemize}
+   The domain bathymetry is read from a file that contains a 2D (x,y)
+   map of depths (in m) for the ocean or pressures (in Pa) for the
- The domain bathymetry is read from a file that contains a 2D (x,y) map of
+   atmosphere. The file name is represented by the variable
- depths (in m) for the ocean or pressures (in Pa) for the atmosphere. The
+   \textbf{bathyFile}\textit{. }The file is assumed to contain binary
- file name is represented by the variable \textbf{bathyFile}\textit{. }The
+   numbers giving the depth (pressure) of the model at each grid cell,
- file is assumed to contain binary numbers giving the depth (pressure) of the
+   ordered with the x coordinate varying fastest. The points are
- model at each grid cell, ordered with the x coordinate varying fastest. The
+   ordered from low coordinate to high coordinate for both axes. The
- points are ordered from low coordinate to high coordinate for both axes. The
+   model code applies without modification to enclosed, periodic, and
- model code applies without modification to enclosed, periodic, and double
+   double periodic domains. Periodicity is assumed by default and is
- periodic domains. Periodicity is assumed by default and is suppressed by
+   suppressed by setting the depths to 0m for the cells at the limits
- setting the depths to 0m for the cells at the limits of the computational
+   of the computational domain (note: not sure this is the case for the
- domain (note: not sure this is the case for the atmosphere). The precision
+   atmosphere). The precision with which to read the binary data is
- with which to read the binary data is controlled by the integer variable
+   controlled by the integer variable \textbf{readBinaryPrec }which can
- \textbf{readBinaryPrec }which can take the value \texttt{32} (single
+   take the value \texttt{32} (single precision) or \texttt{64} (double
- precision) or \texttt{64} (double precision). See the matlab program \textit{%
+   precision). See the matlab program \textit{ gendata.m }in the
- gendata.m }in the \textit{input }directories under \textit{verification }to
+   \textit{input }directories under \textit{verification }to see how
- see how the bathymetry files are generated for the case study experiments.
+   the bathymetry files are generated for the case study experiments.
- To use the partial cell capability, the variable \textbf{hFacMin}\textit{\ }%
+   To use the partial cell capability, the variable
- needs to be set to a value between 0 and 1 (it is set to 1 by default)
+   \textbf{hFacMin}\textit{\ } needs to be set to a value between 0 and
- corresponding to the minimum fractional size of the cell. For example if the
+(it is set to 1 by default) corresponding to the minimum
- bottom cell is 500m thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the
+   fractional size of the cell. For example if the bottom cell is 500m
- actual thickness of the cell (i.e. used in the code) can cover a range of
+   thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the actual
- discrete values 50m apart from 50m to 500m depending on the value of the
+   thickness of the cell (i.e. used in the code) can cover a range of
- bottom depth (in \textbf{bathyFile}) at this point.
+   discrete values 50m apart from 50m to 500m depending on the value of
+   the bottom depth (in \textbf{bathyFile}) at this point.
- Note that the bottom depths (or pressures) need not coincide with the models
- levels as deduced from \textbf{delz}\textit{\ }or\textit{\ }\textbf{delp}%
+   Note that the bottom depths (or pressures) need not coincide with
- \textit{. }The model will interpolate the numbers in \textbf{bathyFile}%
+   the models levels as deduced from \textbf{delz}\textit{\
- \textit{\ }so that they match the levels obtained from \textbf{delz}\textit{%
+   }or\textit{\ }\textbf{delp} \textit{. }The model will interpolate
- \ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
+   the numbers in \textbf{bathyFile} \textit{\ }so that they match the
+   levels obtained from \textbf{delz}\textit{ \ }or\textit{\
- (Note: the atmospheric case is a bit more complicated than what is written
+   }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
- here I think. To come soon...)
+   (Note: the atmospheric case is a bit more complicated than what is
+   written here I think. To come soon...)
+ \item[time-discretization] \
+   The time steps are set through the real variables \textbf{deltaTMom}
+   and \textbf{deltaTtracer} (in s) which represent the time step for
+   the momentum and tracer equations, respectively. For synchronous
+   integrations, simply set the two variables to the same value (or you
+   can prescribe one time step only through the variable
+   \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
+   through the variable \textbf{abEps} (dimensionless). The stagger
+   baroclinic time stepping can be activated by setting the logical
+   variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
- \begin{itemize}
+ \end{description}
- \item time-discretization
- \end{itemize}
- The time steps are set through the real variables \textbf{deltaTMom}
- and \textbf{deltaTtracer} (in s) which represent the time step for the
- momentum and tracer equations, respectively. For synchronous
- integrations, simply set the two variables to the same value (or you
- can prescribe one time step only through the variable
- \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
- through the variable \textbf{abEps} (dimensionless). The stagger
- baroclinic time stepping can be activated by setting the logical
- variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
  \subsection{Equation of state}
-Line 991 
 useCoriolis, momPressureForcing, momStep
+Line 1101 
 useCoriolis, momPressureForcing, momStep
  Look at the file \textit{model/inc/PARAMS.h }for a precise definition of
  these variables.
- \begin{itemize}
+ \begin{description}
- \item initialization
+ \item[initialization] \
- \end{itemize}
+   The velocity components are initialized to 0 unless the simulation
- The velocity components are initialized to 0 unless the simulation is
+   is starting from a pickup file (see section on simulation control
- starting from a pickup file (see section on simulation control parameters).
+   parameters).
- \begin{itemize}
+ \item[forcing] \
- \item forcing
- \end{itemize}
+   This section only applies to the ocean. You need to generate
+   wind-stress data into two files \textbf{zonalWindFile}\textit{\ }and
- This section only applies to the ocean. You need to generate wind-stress
+   \textbf{ meridWindFile }corresponding to the zonal and meridional
- data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{%
+   components of the wind stress, respectively (if you want the stress
- meridWindFile }corresponding to the zonal and meridional components of the
+   to be along the direction of only one of the model horizontal axes,
- wind stress, respectively (if you want the stress to be along the direction
+   you only need to generate one file). The format of the files is
- of only one of the model horizontal axes, you only need to generate one
+   similar to the bathymetry file. The zonal (meridional) stress data
- file). The format of the files is similar to the bathymetry file. The zonal
+   are assumed to be in Pa and located at U-points (V-points). As for
- (meridional) stress data are assumed to be in Pa and located at U-points
+   the bathymetry, the precision with which to read the binary data is
- (V-points). As for the bathymetry, the precision with which to read the
+   controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } See
- binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ }
+   the matlab program \textit{gendata.m }in the \textit{input
- See the matlab program \textit{gendata.m }in the \textit{input }directories
+   }directories under \textit{verification }to see how simple
- under \textit{verification }to see how simple analytical wind forcing data
+   analytical wind forcing data are generated for the case study
- are generated for the case study experiments.
+   experiments.
- There is also the possibility of prescribing time-dependent periodic
+   There is also the possibility of prescribing time-dependent periodic
- forcing. To do this, concatenate the successive time records into a single
+   forcing. To do this, concatenate the successive time records into a
- file (for each stress component) ordered in a (x, y, t) fashion and set the
+   single file (for each stress component) ordered in a (x, y, t)
- following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
+   fashion and set the following variables:
- \textbf{externForcingPeriod }to the period (in s) of which the forcing
+   \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
- varies (typically 1 month), and \textbf{externForcingCycle }to the repeat
+   \textbf{externForcingPeriod }to the period (in s) of which the
- time (in s) of the forcing (typically 1 year -- note: \textbf{%
+   forcing varies (typically 1 month), and \textbf{externForcingCycle
- externForcingCycle }must be a multiple of \textbf{externForcingPeriod}).
+   }to the repeat time (in s) of the forcing (typically 1 year -- note:
- With these variables set up, the model will interpolate the forcing linearly
+   \textbf{ externForcingCycle }must be a multiple of
- at each iteration.
+   \textbf{externForcingPeriod}).  With these variables set up, the
+   model will interpolate the forcing linearly at each iteration.
- \begin{itemize}
- \item dissipation
+ \item[dissipation] \
- \end{itemize}
+   The lateral eddy viscosity coefficient is specified through the
- The lateral eddy viscosity coefficient is specified through the variable
+   variable \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The
- \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity
+   vertical eddy viscosity coefficient is specified through the
- coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$%
+   variable \textbf{viscAz }(in m$^{2}$s$ ^{-1}$) for the ocean and
- ^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$)
+   \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) for the atmosphere.
- for the atmosphere. The vertical diffusive fluxes can be computed implicitly
+   The vertical diffusive fluxes can be computed implicitly by setting
- by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}%
+   the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}
- .'. In addition, biharmonic mixing can be added as well through the variable
+   .'. In addition, biharmonic mixing can be added as well through the
- \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid,
+   variable \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a
- you might also need to set the variable \textbf{cosPower} which is set to 0
+   spherical polar grid, you might also need to set the variable
- by default and which represents the power of cosine of latitude to multiply
+   \textbf{cosPower} which is set to 0 by default and which represents
- viscosity. Slip or no-slip conditions at lateral and bottom boundaries are
+   the power of cosine of latitude to multiply viscosity. Slip or
- specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }%
+   no-slip conditions at lateral and bottom boundaries are specified
- and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip
+   through the logical variables \textbf{no\_slip\_sides}\textit{\ }
- boundary conditions are applied. If no-slip boundary conditions are applied
+   and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}',
- at the bottom, a bottom drag can be applied as well. Two forms are
+   free-slip boundary conditions are applied. If no-slip boundary
- available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$%
+   conditions are applied at the bottom, a bottom drag can be applied
- ^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{%
+   as well. Two forms are available: linear (set the variable
- \ }in m$^{-1}$).
+   \textbf{bottomDragLinear}\textit{\ }in s$ ^{-1}$) and quadratic (set
+   the variable \textbf{bottomDragQuadratic}\textit{ \ }in m$^{-1}$).
- The Fourier and Shapiro filters are described elsewhere.
+   The Fourier and Shapiro filters are described elsewhere.
- \begin{itemize}
- \item C-D scheme
+ \item[C-D scheme] \
- \end{itemize}
+   If you run at a sufficiently coarse resolution, you will need the
+   C-D scheme for the computation of the Coriolis terms. The
+   variable\textbf{\ tauCD}, which represents the C-D scheme coupling
+   timescale (in s) needs to be set.
+ \item[calculation of pressure/geopotential] \
+   First, to run a non-hydrostatic ocean simulation, set the logical
+   variable \textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure
+   field is then inverted through a 3D elliptic equation. (Note: this
+   capability is not available for the atmosphere yet.) By default, a
+   hydrostatic simulation is assumed and a 2D elliptic equation is used
+   to invert the pressure field. The parameters controlling the
+   behaviour of the elliptic solvers are the variables
+   \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual } for
+   the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{
+     cg3dTargetResidual }for the 3D case. You probably won't need to
+   alter the default values (are we sure of this?).
+   For the calculation of the surface pressure (for the ocean) or
+   surface geopotential (for the atmosphere) you need to set the
+   logical variables \textbf{rigidLid} and
+   \textbf{implicitFreeSurface}\textit{\ }(set one to '.
+   \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how
+   you want to deal with the ocean upper or atmosphere lower boundary).
- If you run at a sufficiently coarse resolution, you will need the C-D scheme
+ \end{description}
- for the computation of the Coriolis terms. The variable\textbf{\ tauCD},
- which represents the C-D scheme coupling timescale (in s) needs to be set.
- \begin{itemize}
- \item calculation of pressure/geopotential
- \end{itemize}
- First, to run a non-hydrostatic ocean simulation, set the logical variable
- \textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure field is then
- inverted through a 3D elliptic equation. (Note: this capability is not
- available for the atmosphere yet.) By default, a hydrostatic simulation is
- assumed and a 2D elliptic equation is used to invert the pressure field. The
- parameters controlling the behaviour of the elliptic solvers are the
- variables \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual }%
- for the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{%
- cg3dTargetResidual }for the 3D case. You probably won't need to alter the
- default values (are we sure of this?).
- For the calculation of the surface pressure (for the ocean) or surface
- geopotential (for the atmosphere) you need to set the logical variables
- \textbf{rigidLid} and \textbf{implicitFreeSurface}\textit{\ }(set one to '.%
- \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you
- want to deal with the ocean upper or atmosphere lower boundary).
  \subsection{Tracer equations}
-Line 1086 
 This section covers the tracer equations
+Line 1198 
 This section covers the tracer equations
  equation and the salinity (for the ocean) or specific humidity (for the
  atmosphere) equation. As for the momentum equations, we only describe for
  now the parameters that you are likely to change. The logical variables
- \textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{%
+ \textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{
  tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off
  terms in the temperature equation (same thing for salinity or specific
- humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{%
+ humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{
  saltAdvection}\textit{\ }etc). These variables are all assumed here to be
  set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a
  precise definition.
- \begin{itemize}
+ \begin{description}
- \item initialization
+ \item[initialization] \
- \end{itemize}
+   The initial tracer data can be contained in the binary files
- The initial tracer data can be contained in the binary files \textbf{%
+   \textbf{ hydrogThetaFile }and \textbf{hydrogSaltFile}. These files
- hydrogThetaFile }and \textbf{hydrogSaltFile}. These files should contain 3D
+   should contain 3D data ordered in an (x, y, r) fashion with k=1 as
- data ordered in an (x, y, r) fashion with k=1 as the first vertical level.
+   the first vertical level.  If no file names are provided, the
- If no file names are provided, the tracers are then initialized with the
+   tracers are then initialized with the values of \textbf{tRef }and
- values of \textbf{tRef }and \textbf{sRef }mentioned above (in the equation
+   \textbf{sRef }mentioned above (in the equation of state section). In
- of state section). In this case, the initial tracer data are uniform in x
+   this case, the initial tracer data are uniform in x and y for each
- and y for each depth level.
+   depth level.
- \begin{itemize}
+ \item[forcing] \
- \item forcing
- \end{itemize}
+   This part is more relevant for the ocean, the procedure for the
+   atmosphere not being completely stabilized at the moment.
- This part is more relevant for the ocean, the procedure for the atmosphere
- not being completely stabilized at the moment.
+   A combination of fluxes data and relaxation terms can be used for
+   driving the tracer equations. \ For potential temperature, heat flux
- A combination of fluxes data and relaxation terms can be used for driving
+   data (in W/m$ ^{2}$) can be stored in the 2D binary file
- the tracer equations. \ For potential temperature, heat flux data (in W/m$%
+   \textbf{surfQfile}\textit{. }  Alternatively or in addition, the
- ^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }%
+   forcing can be specified through a relaxation term. The SST data to
- Alternatively or in addition, the forcing can be specified through a
+   which the model surface temperatures are restored to are supposed to
- relaxation term. The SST data to which the model surface temperatures are
+   be stored in the 2D binary file \textbf{ thetaClimFile}\textit{.
- restored to are supposed to be stored in the 2D binary file \textbf{%
+   }The corresponding relaxation time scale coefficient is set through
- thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient
+   the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The same
- is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The
+   procedure applies for salinity with the variable names
- same procedure applies for salinity with the variable names \textbf{EmPmRfile%
+   \textbf{EmPmRfile }\textit{, }\textbf{saltClimFile}\textit{, }and
- }\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}%
+   \textbf{tauSaltClimRelax} \textit{\ }for freshwater flux (in m/s)
- \textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data
+   and surface salinity (in ppt) data files and relaxation time scale
- files and relaxation time scale coefficient (in s), respectively. Also for
+   coefficient (in s), respectively. Also for salinity, if the CPP key
- salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural
+   \textbf{USE\_NATURAL\_BCS} is turned on, natural boundary conditions
- boundary conditions are applied i.e. when computing the surface salinity
+   are applied i.e. when computing the surface salinity tendency, the
- tendency, the freshwater flux is multiplied by the model surface salinity
+   freshwater flux is multiplied by the model surface salinity instead
- instead of a constant salinity value.
+   of a constant salinity value.
- As for the other input files, the precision with which to read the data is
+   As for the other input files, the precision with which to read the
- controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic
+   data is controlled by the variable \textbf{readBinaryPrec}.
- forcing can be applied as well following the same procedure used for the
+   Time-dependent, periodic forcing can be applied as well following
- wind forcing data (see above).
+   the same procedure used for the wind forcing data (see above).
- \begin{itemize}
+ \item[dissipation] \
- \item dissipation
- \end{itemize}
+   Lateral eddy diffusivities for temperature and salinity/specific
+   humidity are specified through the variables \textbf{diffKhT }and
- Lateral eddy diffusivities for temperature and salinity/specific humidity
+   \textbf{diffKhS } (in m$^{2}$/s). Vertical eddy diffusivities are
- are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }%
+   specified through the variables \textbf{diffKzT }and \textbf{diffKzS
- (in m$^{2}$/s). Vertical eddy diffusivities are specified through the
+   }(in m$^{2}$/s) for the ocean and \textbf{diffKpT }and
- variables \textbf{diffKzT }and \textbf{diffKzS }(in m$^{2}$/s) for the ocean
+   \textbf{diffKpS }(in Pa$^{2}$/s) for the atmosphere. The vertical
- and \textbf{diffKpT }and \textbf{diffKpS }(in Pa$^{2}$/s) for the
+   diffusive fluxes can be computed implicitly by setting the logical
- atmosphere. The vertical diffusive fluxes can be computed implicitly by
+   variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'. In
- setting the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
+   addition, biharmonic diffusivities can be specified as well through
- .'. In addition, biharmonic diffusivities can be specified as well through
+   the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in
- the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in m$^{4}$/s). Note
+   m$^{4}$/s). Note that the cosine power scaling (specified through
- that the cosine power scaling (specified through \textbf{cosPower }- see the
+   \textbf{cosPower }- see the momentum equations section) is applied
- momentum equations section) is applied to the tracer diffusivities
+   to the tracer diffusivities (Laplacian and biharmonic) as well. The
- (Laplacian and biharmonic) as well. The Gent and McWilliams parameterization
+   Gent and McWilliams parameterization for oceanic tracers is
- for oceanic tracers is described in the package section. Finally, note that
+   described in the package section. Finally, note that tracers can be
- tracers can be also subject to Fourier and Shapiro filtering (see the
+   also subject to Fourier and Shapiro filtering (see the corresponding
- corresponding section on these filters).
+   section on these filters).
- \begin{itemize}
+ \item[ocean convection] \
- \item ocean convection
- \end{itemize}
+   Two options are available to parameterize ocean convection: one is
+   to use the convective adjustment scheme. In this case, you need to
+   set the variable \textbf{cadjFreq}, which represents the frequency
+   (in s) with which the adjustment algorithm is called, to a non-zero
+   value (if set to a negative value by the user, the model will set it
+   to the tracer time step). The other option is to parameterize
+   convection with implicit vertical diffusion. To do this, set the
+   logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'
+   and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s)
+   you wish the tracer vertical diffusivities to have when mixing
+   tracers vertically due to static instabilities. Note that
+   \textbf{cadjFreq }and \textbf{ivdc\_kappa }can not both have
+   non-zero value.
- Two options are available to parameterize ocean convection: one is to use
+ \end{description}
- the convective adjustment scheme. In this case, you need to set the variable
- \textbf{cadjFreq}, which represents the frequency (in s) with which the
- adjustment algorithm is called, to a non-zero value (if set to a negative
- value by the user, the model will set it to the tracer time step). The other
- option is to parameterize convection with implicit vertical diffusion. To do
- this, set the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
- .' and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s) you
- wish the tracer vertical diffusivities to have when mixing tracers
- vertically due to static instabilities. Note that \textbf{cadjFreq }and
- \textbf{ivdc\_kappa }can not both have non-zero value.
  \subsection{Simulation controls}
-Line 1180 
 Typically, you will set it to the tracer
+Line 1294 
 Typically, you will set it to the tracer
  Frequency of checkpointing and dumping of the model state are referenced to
  this clock (see below).
- \begin{itemize}
+ \begin{description}
- \item run duration
+ \item[run duration] \
- \end{itemize}
+   The beginning of a simulation is set by specifying a start time (in
- The beginning of a simulation is set by specifying a start time (in s)
+   s) through the real variable \textbf{startTime }or by specifying an
- through the real variable \textbf{startTime }or by specifying an initial
+   initial iteration number through the integer variable
- iteration number through the integer variable \textbf{nIter0}. If these
+   \textbf{nIter0}. If these variables are set to nonzero values, the
- variables are set to nonzero values, the model will look for a ''pickup''
+   model will look for a ''pickup'' file \textit{pickup.0000nIter0 }to
- file \textit{pickup.0000nIter0 }to restart the integration\textit{. }The end
+   restart the integration\textit{. }The end of a simulation is set
- of a simulation is set through the real variable \textbf{endTime }(in s).
+   through the real variable \textbf{endTime }(in s).  Alternatively,
- Alternatively, you can specify instead the number of time steps to execute
+   you can specify instead the number of time steps to execute through
- through the integer variable \textbf{nTimeSteps}.
+   the integer variable \textbf{nTimeSteps}.
+ \item[frequency of output] \
+   Real variables defining frequencies (in s) with which output files
+   are written on disk need to be set up. \textbf{dumpFreq }controls
+   the frequency with which the instantaneous state of the model is
+   saved. \textbf{chkPtFreq } and \textbf{pchkPtFreq }control the
+   output frequency of rolling and permanent checkpoint files,
+   respectively. See section 1.5.1 Output files for the definition of
+   model state and checkpoint files. In addition, time-averaged fields
+   can be written out by setting the variable \textbf{taveFreq} (in s).
+   The precision with which to write the binary data is controlled by
+   the integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32}
+   or \texttt{ 64}).
- \begin{itemize}
+ \end{description}
- \item frequency of output
- \end{itemize}
- Real variables defining frequencies (in s) with which output files are
- written on disk need to be set up. \textbf{dumpFreq }controls the frequency
- with which the instantaneous state of the model is saved. \textbf{chkPtFreq }%
- and \textbf{pchkPtFreq }control the output frequency of rolling and
- permanent checkpoint files, respectively. See section 1.5.1 Output files for the
- definition of model state and checkpoint files. In addition, time-averaged
- fields can be written out by setting the variable \textbf{taveFreq} (in s).
- The precision with which to write the binary data is controlled by the
- integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%
-}).
  %%% Local Variables:
  %%% mode: latex

 Legend:



Removed from v.1.15
 


changed lines


 
Added in v.1.17
 Legend:



Removed from v.1.15
 


changed lines


 
Added in v.1.17
-Removed from v.1.15
+Added in v.1.17

	ViewVC Help
Powered by ViewVC 1.1.22