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

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-revision 1.2 by adcroft,
Fri Sep 28 15:46:09 2001 UTC
+revision 1.14 by edhill,
Wed Jul 30 13:42:52 2003 UTC
 Line 1
  % $Header$
  % $Name$
- \section{Getting started}
+ %\section{Getting started}
- In this part, we describe how to use the model. In the first section, we
+ In this section, we describe how to use the model. In the first
- provide enough information to help you get started with the model. We
+ section, we provide enough information to help you get started with
- believe the best way to familiarize yourself with the model is to run the
+ the model. We believe the best way to familiarize yourself with the
- case study examples provided with the base version. Information on how to
+ model is to run the case study examples provided with the base
- obtain, compile, and run the code is found there as well as a brief
+ version. Information on how to obtain, compile, and run the code is
- description of the model structure directory and the case study examples.
+ found there as well as a brief description of the model structure
- The latter and the code structure are described more fully in sections 2 and
+ directory and the case study examples.  The latter and the code
-, respectively. In section 4, we provide information on how to customize
+ structure are described more fully in chapters
- the code when you are ready to try implementing the configuration you have
+ \ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in
- in mind.
+ this section, we provide information on how to customize the code when
+ you are ready to try implementing the configuration you have in mind.
- \subsection{Obtaining the code}
+ \section{Where to find information}
- The reference web site for the model is:
+ \label{sect:whereToFindInfo}
- \begin{verbatim}
- http://mitgcm.org
+ A web site is maintained for release 1 (Sealion) of MITgcm:
- \end{verbatim}
+ \begin{verbatim}
+ http://mitgcm.org/sealion
- On this site, you can download the model as well as find useful information,
+ \end{verbatim}
- some of which might overlap with what is written here. There is also a
+ Here you will find an on-line version of this document, a
- support news group for the model located at (send your message to \texttt{%
+ ``browsable'' copy of the code and a searchable database of the model
- support@mitgcm.org}):
+ and site, as well as links for downloading the model and
+ documentation, to data-sources and other related sites.
+ There is also a support news group for the model that you can email at
+ \texttt{MITgcm-support@mitgcm.org} or browse at:
  \begin{verbatim}
  news://mitgcm.org/mitgcm.support
  \end{verbatim}
+ A mail to the email list will reach all the developers and be archived
+ on the newsgroup. A users email list will be established at some time
+ in the future.
+ \section{Obtaining the code}
+ \label{sect:obtainingCode}
+ MITgcm can be downloaded from our system by following
+ the instructions below. As a courtesy we ask that you send e-mail to us at
+ \begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml}
+ MITgcm-support@mitgcm.org
+ \begin{rawhtml} </A> \end{rawhtml}
+ to enable us to keep track of who's using the model and in what application.
+ You can download the model two ways:
+ \begin{enumerate}
+ \item Using CVS software. CVS is a freely available source code management
+ tool. To use CVS you need to have the software installed. Many systems
+ come with CVS pre-installed, otherwise good places to look for
+ the software for a particular platform are
+ \begin{rawhtml} <A href=http://www.cvshome.org/ target="idontexist"> \end{rawhtml}
+ cvshome.org
+ \begin{rawhtml} </A> \end{rawhtml}
+ and
+ \begin{rawhtml} <A href=http://www.wincvs.org/ target="idontexist"> \end{rawhtml}
+ wincvs.org
+ \begin{rawhtml} </A> \end{rawhtml}
+ .
+ \item Using a tar file. This method is simple and does not
+ require any special software. However, this method does not
+ provide easy support for maintenance updates.
+ \end{enumerate}
  If CVS is available on your system, we strongly encourage you to use it. CVS
  provides an efficient and elegant way of organizing your code and keeping
  track of your changes. If CVS is not available on your machine, you can also
  download a tar file.
- \subsubsection{using CVS}
  Before you can use CVS, the following environment variable has to be set in
  your .cshrc or .tcshrc:
  \begin{verbatim}
  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
+ \end{verbatim}
+ To start using CVS, register with the MITgcm CVS server using command:
+ \begin{verbatim}
  % cvs login ( CVS password: cvsanon )
  \end{verbatim}
+ You only need to do ``cvs login'' once.
- You only need to do ``cvs login'' once. To obtain the latest source:
+ To obtain the sources for release1 type:
  \begin{verbatim}
- % cvs co -d directory models/MITgcmUV
+ % cvs co -d directory -P -r release1_beta1 MITgcm
  \end{verbatim}
  This creates a directory called \textit{directory}. If \textit{directory}
  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 track of your file versions with
- respect to the repository. Don't edit the files in \textit{CVS}! To obtain a
+ respect to the repository. Don't edit the files in \textit{CVS}!
- specific \textit{version} that is not the latest source:
+ You can also use CVS to download code updates.  More extensive
- \begin{verbatim}
+ information on using CVS for maintaining MITgcm code can be found
- % cvs co -d directory -r version models/MITgcmUV
+ \begin{rawhtml} <A href=http://mitgcm.org/usingcvstoget.html target="idontexist"> \end{rawhtml}
- \end{verbatim}
+ here
+ \begin{rawhtml} </A> \end{rawhtml}
+ .
- \subsubsection{other methods}
- You can download the model as a tar file from the reference web site at:
+ \paragraph*{Conventional download method}
+ \label{sect:conventionalDownload}
+ If you do not have CVS on your system, you can download the model as a
+ tar file from the reference web site at:
+ \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
  \begin{verbatim}
  http://mitgcm.org/download/
  \end{verbatim}
+ \begin{rawhtml} </A> \end{rawhtml}
- \subsection{Model and directory structure}
+ The tar file still contains CVS information which we urge you not to
+ delete; even if you do not use CVS yourself the information can help
- The ``numerical'' model is contained within a execution environment support
+ us if you should need to send us your copy of the code.
- wrapper. This wrapper is designed to provide a general framework for
- grid-point models. MITgcmUV is a specific numerical model that uses the
+ \paragraph*{Upgrading from an earlier version}
- framework. Under this structure the model is split into execution
- environment support code and conventional numerical model code. The
+ If you already have an earlier version of the code you can ``upgrade''
- execution environment support code is held under the \textit{eesupp}
+ your copy instead of downloading the entire repository again. First,
- directory. The grid point model code is held under the \textit{model}
+ ``cd'' (change directory) to the top of your working copy:
- directory. Code execution actually starts in the \textit{eesupp} routines
+ \begin{verbatim}
- and not in the \textit{model} routines. For this reason the top-level
+ % cd MITgcm
+ \end{verbatim}
+ and then issue the cvs update command:
+ \begin{verbatim}
+ % cvs -q update -r release1_beta1 -d -P
+ \end{verbatim}
+ This will update the ``tag'' to ``release1\_beta1'', 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
+ will try to merge your changes with the upgrades. If there is a
+ conflict between your modifications and the upgrade, it will report
+ that file with a ``C'' in front, e.g.:
+ \begin{verbatim}
+ C model/src/ini_parms.F
+ \end{verbatim}
+ If the list of conflicts scrolled off the screen, you can re-issue the
+ cvs update command and it will report the conflicts. Conflicts are
+ indicated in the code by the delimites ``<<<<<<<'', ``======='' and
+ ``>>>>>>>''. For example,
+ \begin{verbatim}
+ <<<<<<< ini_parms.F
+      & bottomDragLinear,myOwnBottomDragCoefficient,
+ =======
+      & 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:
+ \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.
+ \paragraph*{Upgrading to the current pre-release version}
+ We don't make a ``release'' for every little patch and bug fix in
+ order to keep the frequency of upgrades to a minimum. However, if you
+ have run into a problem for which ``we have already fixed in the
+ latest code'' and we haven't made a ``tag'' or ``release'' since that
+ patch then you'll need to get the latest code:
+ \begin{verbatim}
+ % cvs -q update -A -d -P
+ \end{verbatim}
+ Unlike, the ``check-out'' and ``update'' procedures above, there is no
+ ``tag'' or release name. The -A tells CVS to upgrade to the
+ very latest version. As a rule, we don't recommend this since you
+ might upgrade while we are in the processes of checking in the code so
+ that you may only have part of a patch. Using this method of updating
+ also means we can't tell what version of the code you are working
+ with. So please be sure you understand what you're doing.
+ \section{Model and directory structure}
+ The ``numerical'' model is contained within a execution environment
+ support wrapper. This wrapper is designed to provide a general
+ framework for grid-point models. MITgcmUV is a specific numerical
+ 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
+ \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
  \textit{MAIN.F} is in the \textit{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%
-Line 88 
 directory in which to compile the code.
+Line 202 
 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
- \textit{src} that contain include files (*.\textit{h} files) and fortran
+ \textit{src} that contain include files (*.\textit{h} files) and Fortran
  subroutines (*.\textit{F} files), respectively.
  \item \textit{doc}: contains brief documentation notes.
-Line 115 
 the makefile specific to the Tangent lin
+Line 229 
 the makefile specific to the Tangent lin
  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 compute
+ subdirectory \textit{knudsen2} contains code and a makefile that
- coefficients of the polynomial approximation to the knudsen formula for an
+ compute coefficients of the polynomial approximation to the knudsen
- ocean nonlinear equation of state. The \textit{matlab} subdirectory contains
+ formula for an ocean nonlinear equation of state. The \textit{matlab}
- matlab scripts for reading model output directly into matlab. \textit{scripts%
+ subdirectory contains matlab scripts for reading model output directly
- } contains C-shell post-processing scripts for joining processor-based and
+ into matlab. \textit{scripts} contains C-shell post-processing
- tiled-based model output.
+ scripts for joining processor-based and tiled-based model output.
  \item \textit{verification}: this directory contains the model examples. See
- below.
+ section \ref{sect:modelExamples}.
  \end{itemize}
- \subsection{Model examples}
+ \section{Example experiments}
+ \label{sect:modelExamples}
- Now that you have successfully downloaded the model code we recommend that
+ The MITgcm distribution comes with a set of twenty-four pre-configured
- you first try to run the examples provided with the base version. You will
+ numerical experiments. Some of these examples experiments are tests of
- probably want to run the example that is the closest to the configuration
+ individual parts of the model code, but many are fully fledged numerical
- you will use eventually. The examples are located in subdirectories under
+ simulations. A few of the examples are used for tutorial documentation
- the directory \textit{verification} and are briefly described below (a full
+ in sections \ref{sect:eg-baro} - \ref{sect:eg-global}. The other examples
- description is given in section 2):
+ follow the same general structure as the tutorial examples. However,
+ they only include brief instructions in a text file called {\it README}.
+ The examples are located in subdirectories under
+ the directory \textit{verification}. Each
+ example is briefly described below.
- \subsubsection{List of model examples}
+ \subsection{Full list of model examples}
- \begin{itemize}
+ \begin{enumerate}
  \item \textit{exp0} - single layer, ocean double gyre (barotropic with
- free-surface).
+ free-surface). This experiment is described in detail in section
+ \ref{sect:eg-baro}.
- \item \textit{exp1} - 4 layers, ocean double gyre.
+ \item \textit{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
- climatological forcing.
+ 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 channel
+ \item \textit{exp4} - Flow over a Gaussian bump in open-water or channel
  with open boundaries.
- \item \textit{exp5} - inhomogenously forced ocean convection in a doubly
+ \item \textit{exp5} - Inhomogenously forced ocean convection in a doubly
  periodic box.
- \item \textit{front\_relax} - relaxation of an ocean thermal front (test for
+ \item \textit{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 boundary
+ \item \textit{internal wave} - Ocean internal wave forced by open boundary
  conditions.
- \item \textit{natl\_box} - eastern subtropical North Atlantic with KPP
+ \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
  scheme; 1 month integration
- \item \textit{hs94.1x64x5} - zonal averaged atmosphere using Held and Suarez
+ \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and Suarez
  '94 forcing.
  \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez
-Line 170 
 scheme; 1 month integration
+Line 292 
 scheme; 1 month integration
  \item \textit{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, 5 layers
+ \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics. Global
- Molteni physics package. Global Zonal Mean configuration, 1x64x5 resolution.
+ Zonal Mean configuration, 1x64x5 resolution.
  \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric
- physics, 5 layers Molteni physics package. Equatorial Slice configuration.
+ physics, equatorial Slice configuration.
 D (X-Z).
  \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
- physics, 5 layers Molteni physics package. 3D Equatorial Channel
+ physics. 3D Equatorial Channel configuration.
- configuration (not completely tested).
- \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers
+ \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
- Molteni physics package. Global configuration, 128x64x5 resolution.
+ Global configuration, on latitude longitude grid with 128x64x5 grid points
+ ($2.8^\circ{\rm degree}$ resolution).
- \item \textit{adjustment.128x64x1}
+ \item \textit{adjustment.128x64x1} Barotropic adjustment
+ problem on latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm degree}$ resolution).
  \item \textit{adjustment.cs-32x32x1}
- \end{itemize}
+ Barotropic adjustment
+ problem on cube sphere grid with 32x32 points per face ( roughly
+ $2.8^\circ{\rm degree}$ resolution).
+ \item \textit{advect\_cs} Two-dimensional passive advection test on
+ cube sphere grid.
+ \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive advection
+ test on Cartesian grid.
+ \item \textit{advect\_yz} Two-dimensional (vertical plane) passive advection test on Cartesian grid.
+ \item \textit{carbon} Simple passive tracer experiment. Includes derivative
+ calculation. Described in detail in section \ref{sect:eg-carbon-ad}.
- \subsubsection{Directory structure of model examples}
+ \item \textit{flt\_example} Example of using float package.
+ \item \textit{global\_ocean.90x40x15} Global circulation with
+ GM, flux boundary conditions and poles.
+ \item \textit{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 sphere
+ grid.
+ \end{enumerate}
+ \subsection{Directory structure of model examples}
  Each example directory has the following subdirectories:
-Line 214 
 In addition, other include files and sub
+Line 364 
 In addition, other include files and sub
  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 mimimum, the \textit{input} directory contains the following
+ example. At a minimum, the \textit{input} directory contains the following
  files:
  \begin{itemize}
-Line 241 
 comparison with your own output when you
+Line 391 
 comparison with your own output when you
  Once you have chosen the example you want to run, you are ready to compile
  the code.
- \subsection{Compiling the code}
+ \section{Building the code}
+ \label{sect:buildingCode}
+ 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
+ \ref{sect:genmake}, that automatically creates the {\em 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
+ 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
+ \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
+ to use the following options when invoking \textit{genmake}:
+ \begin{verbatim}
+ % ../../../tools/genmake  -mods=../code
+ \end{verbatim}
+ Next, create the dependencies:
+ \begin{verbatim}
+ % make depend
+ \end{verbatim}
+ This modifies {\em Makefile} by attaching a [long] list of files on
+ which other files depend. The purpose of this is to reduce
+ re-compilation if and when you start to modify the code. {\tt make
+ depend} also created links from the model source to this directory.
+ Now compile the code:
+ \begin{verbatim}
+ % make
+ \end{verbatim}
+ The {\tt make} command creates an executable called \textit{mitgcmuv}.
+ 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:
+ \begin{verbatim}
+ ./mitgcmuv > output.txt
+ \end{verbatim}
+ where we are re-directing the stream of text output to the file {\em
+ output.txt}.
+ \subsection{Building/compiling the code elsewhere}
+ In the example above (section \ref{sect:buildingCode}) we built the
+ executable in the {\em input} directory of the experiment for
+ convenience. You can also configure and compile the code in other
+ locations, for example on a scratch disk with out having to copy the
+ entire source tree. The only requirement to do so is you have {\tt
+ genmake} in your path or you know the absolute path to {\tt genmake}.
- \subsubsection{The script \textit{genmake}}
+ The following sections outline some possible methods of organizing you
+ 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
+ % make depend
+ % make
+ \end{verbatim}
+ However, to run the model the executable ({\em mitgcmuv}) and input
+ files must be in the same place. If you only have one calculation to make:
+ \begin{verbatim}
+ % cd ../input
+ % cp ../code/mitgcmuv ./
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
+ or if you will be making multiple runs with the same executable:
+ \begin{verbatim}
+ % cd ../
+ % cp -r input run1
+ % cp code/mitgcmuv run1
+ % cd run1
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
+ \subsubsection{Building from a new directory}
+ Since the {\em input} directory contains input files it is often more
+ useful to keep {\em input} pristine and build in a new directory
+ within {\em verification/exp2/}:
+ \begin{verbatim}
+ % cd verification/exp2
+ % mkdir build
+ % cd build
+ % ../../../tools/genmake -mods=../code
+ % make depend
+ % make
+ \end{verbatim}
+ This builds the code exactly as before but this time you need to copy
+ either the executable or the input files or both in order to run the
+ model. For example,
+ \begin{verbatim}
+ % cp ../input/* ./
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
+ or if you tend to make multiple runs with the same executable then
+ running in a new directory each time might be more appropriate:
+ \begin{verbatim}
+ % cd ../
+ % mkdir run1
+ % cp build/mitgcmuv run1/
+ % cp input/* run1/
+ % cd run1
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
+ \subsubsection{Building from on a scratch disk}
+ Model object files and output data can use up large amounts of disk
+ space so it is often the case that you will be operating on a large
+ scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
+ following commands will build the model in {\em /scratch/exp2-run1}:
+ \begin{verbatim}
+ % cd /scratch/exp2-run1
+ % ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
+ % make depend
+ % make
+ \end{verbatim}
+ To run the model here, you'll need the input files:
+ \begin{verbatim}
+ % cp ~/MITgcm/verification/exp2/input/* ./
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
+ As before, you could build in one directory and make multiple runs of
+ the one experiment:
+ \begin{verbatim}
+ % cd /scratch/exp2
+ % mkdir build
+ % cd build
+ % ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
+ % make depend
+ % make
+ % cd ../
+ % cp -r ~/MITgcm/verification/exp2/input run2
+ % cd run2
+ % ./mitgcmuv > output.txt
+ \end{verbatim}
+ \subsection{\textit{genmake}}
+ \label{sect:genmake}
  To compile the code, use the script \textit{genmake} located in the \textit{%
  tools} directory. \textit{genmake} is a script that generates the makefile.
-Line 344 
 For some of the examples, there is a fil
+Line 650 
 For some of the examples, there is a fil
  that particular example. In this way you don't need to type the options when
  invoking \textit{genmake}.
- \subsubsection{Compiling}
- Let's assume that you want to run, say, example \textit{exp2} in the \textit{%
+ \section{Running the model}
- input} directory. To compile the code, type the following commands from the
+ \label{sect:runModel}
- model root tree:
- \begin{verbatim}
- % cd verification/exp2/input
- % ../../../tools/genmake
- % make depend
- % make
- \end{verbatim}
- If there is no \textit{.genmakerc} in the \textit{input} directory, you have
+ If compilation finished succesfuully (section \ref{sect:buildModel})
- to use the following options when invoking \textit{genmake}:
+ then an executable called {\em mitgcmuv} will now exist in the local
- \begin{verbatim}
+ directory.
- % ../../../tools/genmake  -mods=../code
- \end{verbatim}
- In addition, you will probably want to disable some of the packages. Taking
+ To run the model as a single process (ie. not in parallel) simply
- again the case of \textit{exp2}, the full \textit{genmake} command will
+ type:
- probably look like this:
  \begin{verbatim}
- % ../../../tools/genmake  -mods=../code  -disable=kpp,gmredi,aim,...
+ % ./mitgcmuv
  \end{verbatim}
+ The ``./'' is a safe-guard to make sure you use the local executable
- The make command creates an executable called \textit{mitgcmuv}.
+ in case you have others that exist in your path (surely odd if you
+ do!). The above command will spew out many lines of text output to
- Note that you can compile and run the code in another directory than \textit{%
+ your screen.  This output contains details such as parameter values as
- input}. You just need to make sure that you copy the input data files into
+ well as diagnostics such as mean Kinetic energy, largest CFL number,
- the directory where you want to run the model. For example to compile from
+ etc. It is worth keeping this text output with the binary output so we
- \textit{code}:
+ normally re-direct the {\em stdout} stream as follows:
  \begin{verbatim}
- % cd verification/exp2/code
+ % ./mitgcmuv > output.txt
- % ../../../tools/genmake
- % make depend
- % make
  \end{verbatim}
- \subsection{Running the model}
+ For the example experiments in {\em vericication}, 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.
- The first thing to do is to run the code by typing \textit{mitgcmuv} and see
- what happens. You can compare what you get with what is in the \textit{%
- results} directory. Unless noted otherwise, most examples are set up to run
- for a few time steps only so that you can quickly figure out whether the
- model is working or not.
- \subsubsection{Output files}
+ \subsection{Output files}
  The model produces various output files. At a minimum, the instantaneous
  ``state'' of the model is written out, which is made of the following files:
-Line 441 
 as the pickup files but are named differ
+Line 731 
 as the pickup files but are named differ
  used to restart the model but are overwritten every other time they are
  output to save disk space during long integrations.
- \subsubsection{Looking at the output}
+ \subsection{Looking at the output}
  All the model data are written according to a ``meta/data'' file format.
  Each variable is associated with two files with suffix names \textit{.data}
-Line 455 
 written in this format. The matlab scrip
+Line 745 
 written in this format. The matlab scrip
  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads
  the data. Look at the comments inside the script to see how to use it.
- \section{Code structure}
+ Some examples of reading and visualizing some output in {\em Matlab}:
+ \begin{verbatim}
+ % matlab
+ >> H=rdmds('Depth');
+ >> contourf(H');colorbar;
+ >> title('Depth of fluid as used by model');
+ >> eta=rdmds('Eta',10);
+ >> imagesc(eta');axis ij;colorbar;
+ >> title('Surface height at iter=10');
- \section{Doing it yourself: customizing the code}
+ >> eta=rdmds('Eta',[0:10:100]);
+ >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
+ \end{verbatim}
- \subsection{\protect\bigskip Configuration and setup}
+ \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
-Line 469 
 relative to the ''numerical model'' part
+Line 770 
 relative to the ''numerical model'' part
  the ''execution environment'' 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
  defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{%
  model/inc }or in one of the \textit{code }directories of the case study
-Line 485 
 In what follows the parameters are group
+Line 788 
 In what follows the parameters are group
  computational domain, the equations solved in the model, and the simulation
  controls.
- \subsubsection{Computational domain, geometry and time-discretization}
+ \subsection{Computational domain, geometry and time-discretization}
  \begin{itemize}
  \item dimensions
-Line 568 
 here I think. To come soon...)
+Line 871 
 here I think. To come soon...)
  \item time-discretization
  \end{itemize}
- The time steps are set through the real variables \textbf{deltaTMom }and
+ The time steps are set through the real variables \textbf{deltaTMom}
- \textbf{deltaTtracer }(in s) which represent the time step for the momentum
+ and \textbf{deltaTtracer} (in s) which represent the time step for the
- and tracer equations, respectively. For synchronous integrations, simply set
+ momentum and tracer equations, respectively. For synchronous
- the two variables to the same value (or you can prescribe one time step only
+ integrations, simply set the two variables to the same value (or you
- through the variable \textbf{deltaT}). The Adams-Bashforth stabilizing
+ can prescribe one time step only through the variable
- parameter is set through the variable \textbf{abEps }(dimensionless). The
+ \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
- stagger baroclinic time stepping can be activated by setting the logical
+ through the variable \textbf{abEps} (dimensionless). The stagger
- variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'.
+ baroclinic time stepping can be activated by setting the logical
+ variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
- \subsubsection{Equation of state}
+ \subsection{Equation of state}
- First, because the model equations are written in terms of perturbations, a
- reference thermodynamic state needs to be specified. This is done through
+ First, because the model equations are written in terms of
- the 1D arrays \textbf{tRef}\textit{\ }and \textbf{sRef}. \textbf{tRef }%
+ perturbations, a reference thermodynamic state needs to be specified.
- specifies the reference potential temperature profile (in $^{o}$C for
+ This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}.
- the ocean and $^{o}$K for the atmosphere) starting from the level
+ \textbf{tRef} specifies the reference potential temperature profile
- k=1. Similarly, \textbf{sRef}\textit{\ }specifies the reference salinity
+ (in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting
- profile (in ppt) for the ocean or the reference specific humidity profile
+ from the level k=1. Similarly, \textbf{sRef} specifies the reference
- (in g/kg) for the atmosphere.
+ salinity profile (in ppt) for the ocean or the reference specific
+ humidity profile (in g/kg) for the atmosphere.
- The form of the equation of state is controlled by the character variables
- \textbf{buoyancyRelation}\textit{\ }and \textbf{eosType}\textit{. }\textbf{%
+ The form of the equation of state is controlled by the character
- buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and
+ variables \textbf{buoyancyRelation} and \textbf{eosType}.
- needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In
+ \textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and
- this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'.
+ needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations.
- For the ocean, two forms of the equation of state are available: linear (set
+ In this case, \textbf{eosType} must be set to '\texttt{IDEALGAS}'.
- \textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial
+ For the ocean, two forms of the equation of state are available:
- approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\
+ linear (set \textbf{eosType} to '\texttt{LINEAR}') and a polynomial
- }to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the
+ approximation to the full nonlinear equation ( set
- thermal and haline expansion coefficients represented by the variables
+ \textbf{eosType}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear
- \textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(in ppt$%
+ case, you need to specify the thermal and haline expansion
- ^{-1}$). For the nonlinear case, you need to generate a file of polynomial
+ coefficients represented by the variables \textbf{tAlpha}\textit{\
- coefficients called \textit{POLY3.COEFFS. }To do this, use the program
+   }(in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For the nonlinear
- \textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is
+ case, you need to generate a file of polynomial coefficients called
- available in the same directory and you will need to edit the number and the
+ \textit{POLY3.COEFFS}. To do this, use the program
- values of the vertical levels in \textit{knudsen2.f }so that they match
+ \textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is
- those of your configuration). \textit{\ }
+ available in the same directory and you will need to edit the number
+ and the values of the vertical levels in \textit{knudsen2.f} so that
+ they match those of your configuration).
+ There there are also higher polynomials for the equation of state:
+ \begin{description}
+ \item['\texttt{UNESCO}':] The UNESCO equation of state formula of
+   Fofonoff and Millard \cite{fofonoff83}. This equation of state
+   assumes in-situ temperature, which is not a model variable; \emph{its use
+   is therefore discouraged, and it is only listed for completeness}.
+ \item['\texttt{JMD95Z}':] A modified UNESCO formula by Jackett and
+   McDougall \cite{jackett95}, which uses the model variable potential
+   temperature as input. The '\texttt{Z}' indicates that this equation
+   of state uses a horizontally and temporally constant pressure
+   $p_{0}=-g\rho_{0}z$.
+ \item['\texttt{JMD95P}':] A modified UNESCO formula by Jackett and
+   McDougall \cite{jackett95}, which uses the model variable potential
+   temperature as input. The '\texttt{P}' indicates that this equation
+   of state uses the actual hydrostatic pressure of the last time
+   step. Lagging the pressure in this way requires an additional pickup
+   file for restarts.
+ \item['\texttt{MDJWF}':] The new, more accurate and less expensive
+   equation of state by McDougall et~al. \cite{mcdougall03}. It also
+   requires lagging the pressure and therefore an additional pickup
+   file for restarts.
+ \end{description}
+ For none of these options an reference profile of temperature or
+ salinity is required.
- \subsubsection{Momentum equations}
+ \subsection{Momentum equations}
  In this section, we only focus for now on the parameters that you are likely
  to change, i.e. the ones relative to forcing and dissipation for example.
-Line 710 
 geopotential (for the atmosphere) you ne
+Line 1040 
 geopotential (for the atmosphere) you ne
  \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you
  want to deal with the ocean upper or atmosphere lower boundary).
- \subsubsection{Tracer equations}
+ \subsection{Tracer equations}
  This section covers the tracer equations i.e. the potential temperature
  equation and the salinity (for the ocean) or specific humidity (for the
-Line 801 
 wish the tracer vertical diffusivities t
+Line 1131 
 wish the tracer vertical diffusivities t
  vertically due to static instabilities. Note that \textbf{cadjFreq }and
  \textbf{ivdc\_kappa }can not both have non-zero value.
- \subsubsection{Simulation controls}
+ \subsection{Simulation controls}
  The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s)
  which determines the IO frequencies and is used in tagging output.
-Line 837 
 fields can be written out by setting the
+Line 1167 
 fields can be written out by setting the
  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
+ %%% TeX-master: t
+ %%% End:

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