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

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

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-revision 1.30 by edhill,
Sat Oct 16 03:40:13 2004 UTC
+revision 1.34 by edhill,
Sat Apr  8 15:29:05 2006 UTC
 Line 99 
 be set within your shell.  For a csh or
  \begin{verbatim}
  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
  \end{verbatim}
- in your .cshrc or .tcshrc file.  For bash or sh shells, put:
+ in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
+ shells, put:
  \begin{verbatim}
  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
  \end{verbatim}
-Line 125 
 The MITgcm web site contains further dir
+Line 126 
 The MITgcm web site contains further dir
  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 154 
 of CVS aliases
+Line 155 
 of CVS aliases
    \label{tab:cvsModules}
  \end{table}
- The checkout process creates a directory called \textit{MITgcm}. If
+ The checkout process creates a directory called \texttt{MITgcm}. If
- the directory \textit{MITgcm} exists this command updates your code
+ the directory \texttt{MITgcm} exists this command updates your code
  based on the repository. Each directory in the source tree contains a
- directory \textit{CVS}. This information is required by CVS to keep
+ directory \texttt{CVS}. This information is required by CVS to keep
  track of your file versions with respect to the repository. Don't edit
- the files in \textit{CVS}!  You can also use CVS to download code
+ the files in \texttt{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 191 
 delete; even if you do not use CVS yours
+Line 192 
 delete; even if you do not use CVS yours
  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
- \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
+ \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
  MITgcm-support@mitgcm.org
  \begin{rawhtml} </A> \end{rawhtml}
  mailing list.
-Line 273 
 framework for grid-point models. MITgcmU
+Line 274 
 framework for grid-point models. MITgcmU
  model that uses the framework. Under this structure the model is split
  into execution environment support code and conventional numerical
  model code. The execution environment support code is held under the
- \textit{eesupp} directory. The grid point model code is held under the
+ \texttt{eesupp} directory. The grid point model code is held under the
- \textit{model} directory. Code execution actually starts in the
+ \texttt{model} directory. Code execution actually starts in the
- \textit{eesupp} routines and not in the \textit{model} routines. For
+ \texttt{eesupp} routines and not in the \texttt{model} routines. For
- this reason the top-level \textit{MAIN.F} is in the
+ this reason the top-level \texttt{MAIN.F} is in the
- \textit{eesupp/src} directory. In general, end-users should not need
+ \texttt{eesupp/src} directory. In general, end-users should not need
  to worry about this level. The top-level routine for the numerical
- part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is
+ part of the code is in \texttt{model/src/THE\_MODEL\_MAIN.F}. Here is
  a brief description of the directory structure of the model under the
  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
+ \item \texttt{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
+ \item \texttt{diags}: contains the code relative to time-averaged
-   diagnostics. It is subdivided into two subdirectories \textit{inc}
+   diagnostics. It is subdivided into two subdirectories \texttt{inc}
-   and \textit{src} that contain include files (*.\textit{h} files) and
+   and \texttt{src} that contain include files (\texttt{*.h} files) and
-   Fortran subroutines (*.\textit{F} files), respectively.
+   Fortran subroutines (\texttt{*.F} files), respectively.
- \item \textit{doc}: contains brief documentation notes.
+ \item \texttt{doc}: contains brief documentation notes.
- \item \textit{eesupp}: contains the execution environment source code.
+ \item \texttt{eesupp}: contains the execution environment source code.
-   Also subdivided into two subdirectories \textit{inc} and
+   Also subdivided into two subdirectories \texttt{inc} and
-   \textit{src}.
+   \texttt{src}.
- \item \textit{exe}: this directory is initially empty. It is the
+ \item \texttt{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.
+ \item \texttt{model}: this directory contains the main source code.
-   Also subdivided into two subdirectories \textit{inc} and
+   Also subdivided into two subdirectories \texttt{inc} and
-   \textit{src}.
+   \texttt{src}.
- \item \textit{pkg}: contains the source code for the packages. Each
+ \item \texttt{pkg}: contains the source code for the packages. Each
-   package corresponds to a subdirectory. For example, \textit{gmredi}
+   package corresponds to a subdirectory. For example, \texttt{gmredi}
    contains the code related to the Gent-McWilliams/Redi scheme,
-   \textit{aim} the code relative to the atmospheric intermediate
+   \texttt{aim} the code relative to the atmospheric intermediate
    physics. The packages are described in detail in section 3.
- \item \textit{tools}: this directory contains various useful tools.
+ \item \texttt{tools}: this directory contains various useful tools.
-   For example, \textit{genmake2} is a script written in csh (C-shell)
+   For example, \texttt{genmake2} is a script written in csh (C-shell)
    that should be used to generate your makefile. The directory
-   \textit{adjoint} contains the makefile specific to the Tangent
+   \texttt{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
+ \item \texttt{utils}: this directory contains various utilities. The
-   subdirectory \textit{knudsen2} contains code and a makefile that
+   subdirectory \texttt{knudsen2} contains code and a makefile that
    compute coefficients of the polynomial approximation to the knudsen
    formula for an ocean nonlinear equation of state. The
-   \textit{matlab} subdirectory contains matlab scripts for reading
+   \texttt{matlab} subdirectory contains matlab scripts for reading
-   model output directly into matlab. \textit{scripts} contains C-shell
+   model output directly into matlab. \texttt{scripts} contains C-shell
    post-processing scripts for joining processor-based and tiled-based
    model output.
- \item \textit{verification}: this directory contains the model
+ \item \texttt{verification}: this directory contains the model
    examples. See section \ref{sect:modelExamples}.
  \end{itemize}
-Line 342 
 structure).
+Line 343 
 structure).
  %% a set of twenty-four pre-configured numerical experiments
- The MITgcm distribution comes with more than a dozen pre-configured
+ The full MITgcm distribution comes with more than a dozen
- numerical experiments. Some of these example experiments are tests of
+ pre-configured numerical experiments. Some of these example
- individual parts of the model code, but many are fully fledged
+ experiments are tests of individual parts of the model code, but many
- numerical simulations. A few of the examples are used for tutorial
+ are fully fledged numerical simulations. A few of the examples are
- documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.
+ used for tutorial documentation in sections \ref{sect:eg-baro} -
- The other examples follow the same general structure as the tutorial
+ \ref{sect:eg-global}.  The other examples follow the same general
- examples. However, they only include brief instructions in a text file
+ structure as the tutorial examples. However, they only include brief
- called {\it README}.  The examples are located in subdirectories under
+ instructions in a text file called {\it README}.  The examples are
- the directory \textit{verification}. Each example is briefly described
+ located in subdirectories under the directory \texttt{verification}.
- below.
+ Each example is briefly described below.
  \subsection{Full list of model examples}
  \begin{enumerate}
- \item \textit{exp0} - single layer, ocean double gyre (barotropic with
+ \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 \textit{exp1} - Four layer, ocean double gyre. This experiment
+ \item \texttt{exp1} - Four layer, ocean double gyre. This experiment
    is described in detail in section \ref{sect:eg-baroc}.
- \item \textit{exp2} - 4x4 degree global ocean simulation with steady
+ \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 \textit{exp4} - Flow over a Gaussian bump in open-water or
+ \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
    channel with open boundaries.
- \item \textit{exp5} - Inhomogenously forced ocean convection in a
+ \item \texttt{exp5} - Inhomogenously forced ocean convection in a
    doubly periodic box.
- \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
+ \item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for
  Gent/McWilliams scheme). 2D (Y-Z).
- \item \textit{internal wave} - Ocean internal wave forced by open
+ \item \texttt{internal wave} - Ocean internal wave forced by open
    boundary conditions.
- \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
+ \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
    scheme; 1 month integration
- \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and
+ \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
    Suarez '94 forcing.
- \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
+ \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
    Suarez '94 forcing.
- \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
+ \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
    Suarez '94 forcing on the cubed sphere.
- \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
+ \item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
    Global Zonal Mean configuration, 1x64x5 resolution.
- \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
+ \item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
    Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
- \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
+ \item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
    physics. 3D Equatorial Channel configuration.
- \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
+ \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.
    Global configuration, on latitude longitude grid with 128x64x5 grid
-   points ($2.8^\circ{\rm degree}$ resolution).
+   points ($2.8^\circ$ resolution).
- \item \textit{adjustment.128x64x1} Barotropic adjustment problem on
+ \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
-   latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
+   latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
-     degree}$ resolution).
- \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on
+ \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
-   cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
+   cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
-     degree}$ resolution).
+   resolution).
- \item \textit{advect\_cs} Two-dimensional passive advection test on
+ \item \texttt{advect\_cs} Two-dimensional passive advection test on
    cube sphere grid.
- \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive
+ \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
    advection test on Cartesian grid.
- \item \textit{advect\_yz} Two-dimensional (vertical plane) passive
+ \item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
    advection test on Cartesian grid.
- \item \textit{carbon} Simple passive tracer experiment. Includes
+ \item \texttt{carbon} Simple passive tracer experiment. Includes
    derivative calculation. Described in detail in section
    \ref{sect:eg-carbon-ad}.
- \item \textit{flt\_example} Example of using float package.
+ \item \texttt{flt\_example} Example of using float package.
- \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux
+ \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
    boundary conditions and poles.
- \item \textit{global\_ocean\_pressure} Global circulation in pressure
+ \item \texttt{global\_ocean\_pressure} Global circulation in pressure
    coordinate (non-Boussinesq ocean model). Described in detail in
    section \ref{sect:eg-globalpressure}.
- \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube
+ \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
    sphere grid.
  \end{enumerate}
 Line 445 
 Gent/McWilliams scheme). 2D (Y-Z).
  Each example directory has the following subdirectories:
  \begin{itemize}
- \item \textit{code}: contains the code particular to the example. At a
+ \item \texttt{code}: contains the code particular to the example. At a
    minimum, this directory includes the following files:
    \begin{itemize}
-   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
+   \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 \textit{eesupp/inc}.
+     version is located in \texttt{eesupp/inc}.
-   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
+   \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to
      the ``numerical model'' part of the code. The default version is
-     located in \textit{model/inc}.
+     located in \texttt{model/inc}.
-   \item \textit{code/SIZE.h}: declares size of underlying
+   \item \texttt{code/SIZE.h}: declares size of underlying
      computational grid.  The default version is located in
-     \textit{model/inc}.
+     \texttt{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
+   \texttt{code} depending on the particular experiment. See Section 2
    for more details.
- \item \textit{input}: contains the input data files required to run
+ \item \texttt{input}: contains the input data files required to run
-   the example. At a minimum, the \textit{input} directory contains the
+   the example. At a minimum, the \texttt{input} directory contains the
    following files:
    \begin{itemize}
-   \item \textit{input/data}: this file, written as a namelist,
+   \item \texttt{input/data}: this file, written as a namelist,
      specifies the main parameters for the experiment.
-   \item \textit{input/data.pkg}: contains parameters relative to the
+   \item \texttt{input/data.pkg}: contains parameters relative to the
      packages used in the experiment.
-   \item \textit{input/eedata}: this file contains ``execution
+   \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.
-Line 488 
 Each example directory has the following
+Line 497 
 Each example directory has the following
    of the experiment.  This varies from experiment to experiment. See
    section 2 for more details.
- \item \textit{results}: this directory contains the output file
+ \item \texttt{results}: this directory contains the output file
-   \textit{output.txt} produced by the simulation example. This file is
+   \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}
-Line 503 
 compile the code.
+Line 512 
 compile the code.
  <!-- CMIREDIR:buildingCode: -->
  \end{rawhtml}
- To compile the code, we use the {\em make} program. This uses a file
+ To compile the code, we use the \texttt{make} program. This uses a
- ({\em Makefile}) that allows us to pre-process source files, specify
+ file (\texttt{Makefile}) that allows us to pre-process source files,
- compiler and optimization options and also figures out any file
+ specify compiler and optimization options and also figures out any
- dependencies. We supply a script ({\em genmake2}), described in
+ file dependencies. We supply a script (\texttt{genmake2}), described
- section \ref{sect:genmake}, that automatically creates the {\em
+ in section \ref{sect:genmake}, that automatically creates the
-   Makefile} for you. You then need to build the dependencies and
+ \texttt{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
+ As an example, assume that you want to build and run experiment
- \textit{verification/exp2}. The are multiple ways and places to
+ \texttt{verification/exp2}. The are multiple ways and places to
  actually do this but here let's build the code in
- \textit{verification/exp2/input}:
+ \texttt{verification/exp2/build}:
  \begin{verbatim}
- % cd verification/exp2/input
+ % cd verification/exp2/build
  \end{verbatim}
- First, build the {\em Makefile}:
+ First, build the \texttt{Makefile}:
  \begin{verbatim}
  % ../../../tools/genmake2 -mods=../code
  \end{verbatim}
- The command line option tells {\em genmake} to override model source
+ The command line option tells \texttt{genmake} to override model source
- code with any files in the directory {\em ../code/}.
+ code with any files in the directory \texttt{../code/}.
- On many systems, the {\em genmake2} program will be able to
+ On many systems, the \texttt{genmake2} program will be able to
  automatically recognize the hardware, find compilers and other tools
- within the user's path (``echo \$PATH''), and then choose an
+ within the user's path (``\texttt{echo \$PATH}''), and then choose an
  appropriate set of options from the files (``optfiles'') contained in
- the {\em tools/build\_options} directory.  Under some circumstances, a
+ the \texttt{tools/build\_options} directory.  Under some
- user may have to create a new ``optfile'' in order to specify the
+ circumstances, a user may have to create a new ``optfile'' in order to
- exact combination of compiler, compiler flags, libraries, and other
+ specify the exact combination of compiler, compiler flags, libraries,
- options necessary to build a particular configuration of MITgcm.  In
+ and other options necessary to build a particular configuration of
- such cases, it is generally helpful to read the existing ``optfiles''
+ MITgcm.  In such cases, it is generally helpful to read the existing
- and mimic their syntax.
+ ``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}
+ \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:
+ To specify an optfile to \texttt{genmake2}, the syntax is:
  \begin{verbatim}
  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
  \end{verbatim}
- Once a {\em Makefile} has been generated, we create the dependencies:
+ Once a \texttt{Makefile} has been generated, we create the
+ dependencies with the command:
  \begin{verbatim}
  % make depend
  \end{verbatim}
- This modifies the {\em Makefile} by attaching a [long] list of files
+ This modifies the \texttt{Makefile} by attaching a (usually, long)
- upon which other files depend. The purpose of this is to reduce
+ list of files upon which other files depend. The purpose of this is to
- re-compilation if and when you start to modify the code. The {\tt make
+ reduce re-compilation if and when you start to modify the code. The
-   depend} command also creates links from the model source to this
+ {\tt make depend} command also creates links from the model source to
- directory.  It is important to note that the {\tt make depend} stage
+ this directory.  It is important to note that the {\tt make depend}
- will occasionally produce warnings or errors since the dependency
+ stage will occasionally produce warnings or errors since the
- parsing tool is unable to find all of the necessary header files
+ dependency parsing tool is unable to find all of the necessary header
- (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it is
+ files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
- usually OK to ignore the warnings/errors and proceed to the next step.
+ is usually OK to ignore the warnings/errors and proceed to the next
+ step.
- Next compile the code:
+ Next one can compile the code using:
  \begin{verbatim}
  % make
  \end{verbatim}
- The {\tt make} command creates an executable called \textit{mitgcmuv}.
+ The {\tt make} command creates an executable called \texttt{mitgcmuv}.
  Additional make ``targets'' are defined within the makefile to aid in
- the production of adjoint and other versions of MITgcm.
+ the production of adjoint and other versions of MITgcm.  On SMP
+ (shared multi-processor) systems, the build process can often be sped
+ up appreciably using the command:
+ \begin{verbatim}
+ % make -j 2
+ \end{verbatim}
+ where the ``2'' can be replaced with a number that corresponds to the
+ number of CPUs available.
  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:
+ given in section \ref{sect:runModel}. Here, we can run the model by
+ first creating links to all the input files:
+ \begin{verbatim}
+ ln -s ../input/* .
+ \end{verbatim}
+ and then calling the executable with:
  \begin{verbatim}
  ./mitgcmuv > output.txt
  \end{verbatim}
- where we are re-directing the stream of text output to the file {\em
+ where we are re-directing the stream of text output to the file
- output.txt}.
+ \texttt{output.txt}.
  \section[Running MITgcm]{Running the model in prognostic mode}
-Line 587 
 output.txt}.
+Line 610 
 output.txt}.
  <!-- CMIREDIR:runModel: -->
  \end{rawhtml}
- If compilation finished succesfuully (section \ref{sect:buildingCode})
+ If compilation finished succesfully (section \ref{sect:buildingCode})
  then an executable called \texttt{mitgcmuv} will now exist in the
  local directory.
-Line 602 
 do!). The above command will spew out ma
+Line 625 
 do!). The above command will spew out ma
  your screen.  This output contains details such as parameter values as
  well as diagnostics such as mean Kinetic energy, largest CFL number,
  etc. It is worth keeping this text output with the binary output so we
- normally re-direct the {\em stdout} stream as follows:
+ normally re-direct the \texttt{stdout} stream as follows:
  \begin{verbatim}
  % ./mitgcmuv > output.txt
  \end{verbatim}
-Line 610 
 In the event that the model encounters a
+Line 633 
 In the event that the model encounters a
  helpful to include the last few line of this \texttt{output.txt} file
  along with the (\texttt{stderr}) error message within any bug reports.
- For the example experiments in {\em verification}, an example of the
+ For the example experiments in \texttt{verification}, an example of the
- output is kept in {\em results/output.txt} for comparison. You can
+ output is kept in \texttt{results/output.txt} for comparison. You can
- compare your {\em output.txt} with the corresponding one for that
+ compare your \texttt{output.txt} with the corresponding one for that
  experiment to check that the set-up works.
  \subsection{Output files}
- The model produces various output files.  Depending upon the I/O
+ The model produces various output files and, when using \texttt{mnc},
- package selected (either \texttt{mdsio} or \texttt{mnc} or both as
+ sometimes even directories.  Depending upon the I/O package(s)
- determined by both the compile-time settings and the run-time flags in
+ selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
- \texttt{data.pkg}), the following output may appear.
+ both as determined by \texttt{code/packages.conf}) and the run-time
+ flags set (in \texttt{input/data.pkg}), the following output may
+ appear.
  \subsubsection{MDSIO output files}
-Line 632 
 package.  At a minimum, the instantaneou
+Line 657 
 package.  At a minimum, the instantaneou
  written out, which is made of the following files:
  \begin{itemize}
- \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>
+ \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
-$ eastward).
+   and positive eastward).
- \item \textit{V.00000nIter} - meridional component of velocity field (m/s
+ \item \texttt{V.00000nIter} - meridional component of velocity field
- and $> 0$ northward).
+   (m/s and positive northward).
- \item \textit{W.00000nIter} - vertical component of velocity field (ocean:
+ \item \texttt{W.00000nIter} - vertical component of velocity field
- m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure
+   (ocean: m/s and positive upward, atmosphere: Pa/s and positive
- i.e. downward).
+   towards increasing pressure i.e. downward).
- \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,
+ \item \texttt{T.00000nIter} - potential temperature (ocean:
- atmosphere: $^{0}$K).
+   $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
- \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor
+ \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
- (g/kg).
+   vapor (g/kg).
- \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:
+ \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
- surface pressure anomaly (Pa).
+   atmosphere: surface pressure anomaly (Pa).
  \end{itemize}
- The chain \textit{00000nIter} consists of ten figures that specify the
+ The chain \texttt{00000nIter} consists of ten figures that specify the
- iteration number at which the output is written out. For example, \textit{%
+ iteration number at which the output is written out. For example,
- U.0000000300} is the zonal velocity at iteration 300.
+ \texttt{U.0000000300} is the zonal velocity at iteration 300.
  In addition, a ``pickup'' or ``checkpoint'' file called:
  \begin{itemize}
- \item \textit{pickup.00000nIter}
+ \item \texttt{pickup.00000nIter}
  \end{itemize}
  is written out. This file represents the state of the model in a condensed
-Line 667 
 form and is used for restarting the inte
+Line 692 
 form and is used for restarting the inte
  there is an additional ``pickup'' file:
  \begin{itemize}
- \item \textit{pickup\_cd.00000nIter}
+ \item \texttt{pickup\_cd.00000nIter}
  \end{itemize}
  containing the D-grid velocity data and that has to be written out as well
  in order to restart the integration. Rolling checkpoint files are the same
  as the pickup files but are named differently. Their name contain the chain
- \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be
+ \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
  used to restart the model but are overwritten every other time they are
  output to save disk space during long integrations.
-Line 687 
 a name such as \texttt{mnc\_test\_\${DAT
+Line 712 
 a name such as \texttt{mnc\_test\_\${DAT
  within this subdirectory are all in the ``self-describing'' netCDF
  format and can thus be browsed and/or plotted using tools such as:
  \begin{itemize}
- \item At a minimum, the \texttt{ncdump} utility is typically included
+ \item \texttt{ncdump} is a utility which is typically included
    with every netCDF install:
    \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
  \begin{verbatim}
  http://www.unidata.ucar.edu/packages/netcdf/
  \end{verbatim}
-   \begin{rawhtml} </A> \end{rawhtml}
+   \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
+   binaries into formatted ASCII text files.
- \item The \texttt{ncview} utility is a very convenient and quick way
+ \item \texttt{ncview} utility is a very convenient and quick way
    to plot netCDF data and it runs on most OSes:
    \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
  \begin{verbatim}
-Line 705 
 http://meteora.ucsd.edu/~pierce/ncview_h
+Line 731 
 http://meteora.ucsd.edu/~pierce/ncview_h
  \item MatLAB(c) and other common post-processing environments provide
    various netCDF interfaces including:
+   \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
+ \begin{verbatim}
+ http://mexcdf.sourceforge.net/
+ \end{verbatim}
+   \begin{rawhtml} </A> \end{rawhtml}
    \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
  \begin{verbatim}
  http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
  \end{verbatim}
    \begin{rawhtml} </A> \end{rawhtml}
  \end{itemize}
-Line 718 
 http://woodshole.er.usgs.gov/staffpages/
+Line 748 
 http://woodshole.er.usgs.gov/staffpages/
  The ``traditional'' or mdsio model data are written according to a
  ``meta/data'' file format.  Each variable is associated with two files
- with suffix names \textit{.data} and \textit{.meta}. The
+ with suffix names \texttt{.data} and \texttt{.meta}. The
- \textit{.data} file contains the data written in binary form
+ \texttt{.data} file contains the data written in binary form
- (big\_endian by default). The \textit{.meta} file is a ``header'' file
+ (big\_endian by default). The \texttt{.meta} file is a ``header'' file
  that contains information about the size and the structure of the
- \textit{.data} file. This way of organizing the output is particularly
+ \texttt{.data} file. This way of organizing the output is particularly
  useful when running multi-processors calculations. The base version of
  the model includes a few matlab utilities to read output files written
  in this format. The matlab scripts are located in the directory
- \textit{utils/matlab} under the root tree. The script \textit{rdmds.m}
+ \texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m}
  reads the data. Look at the comments inside the script to see how to
  use it.
-Line 745 
 Some examples of reading and visualizing
+Line 775 
 Some examples of reading and visualizing
  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
  \end{verbatim}
- Similar scripts for netCDF output (\texttt{rdmnc.m}) are available.
+ Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
+ they are described in Section \ref{sec:pkg:mnc}.

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