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

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-revision 1.35 by molod,
Thu Apr 20 22:09:08 2006 UTC
+revision 1.38 by molod,
Wed Jun 28 17:20:51 2006 UTC
 Line 21 
 you are ready to try implementing the co
  <!-- CMIREDIR:whereToFindInfo: -->
  \end{rawhtml}
- A web site is maintained for release 2 (``Pelican'') of MITgcm:
+ There is a web-archived support mailing list for the model that
- \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
- \begin{verbatim}
- http://mitgcm.org/pelican
- \end{verbatim}
- \begin{rawhtml} </A> \end{rawhtml}
- Here you will find an on-line version of this document, a
- ``browsable'' copy of the code and a searchable database of the model
- and site, as well as links for downloading the model and
- documentation, to data-sources, and other related sites.
- There is also a web-archived support mailing list for the model that
  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
  \begin{verbatim}
-Line 40 
 http://mitgcm.org/mailman/listinfo/mitgc
+Line 29 
 http://mitgcm.org/mailman/listinfo/mitgc
  http://mitgcm.org/pipermail/mitgcm-support/
  \end{verbatim}
  \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}
- \begin{rawhtml} </A> \end{rawhtml}
- %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
  \section{Obtaining the code}
  \label{sect:obtainingCode}
-Line 175 
 they create can be changed to a differen
+Line 154 
 they create can be changed to a differen
     %  mv MITgcm MITgcm_verif_basic
  \end{verbatim}
- \subsection{Method 2 - Tar file download}
- \label{sect:conventionalDownload}
- If you do not have CVS on your system, you can download the model as a
- tar file from the 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}
- 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
- 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}
- MITgcm-support@mitgcm.org
- \begin{rawhtml} </A> \end{rawhtml}
- mailing list.
  \subsubsection{Upgrading from an earlier version}
  If you already have an earlier version of the code you can ``upgrade''
-Line 262 
 that you may only have part of a patch.
+Line 220 
 that you may only have part of a patch.
  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.
+ \subsection{Method 2 - Tar file download}
+ \label{sect:conventionalDownload}
+ If you do not have CVS on your system, you can download the model as a
+ tar file from the 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}
+ 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
+ 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}
+ MITgcm-support@mitgcm.org
+ \begin{rawhtml} </A> \end{rawhtml}
+ mailing list.
  \section{Model and directory structure}
  \begin{rawhtml}
  <!-- CMIREDIR:directory_structure: -->
-Line 286 
 structure).
+Line 264 
 structure).
  \begin{itemize}
- \item \texttt{bin}: this directory is initially empty. It is the
-   default directory in which to compile the code.
- \item \texttt{diags}: contains the code relative to time-averaged
-   diagnostics. It is subdivided into two subdirectories \texttt{inc}
-   and \texttt{src} that contain include files (\texttt{*.h} files) and
-   Fortran subroutines (\texttt{*.F} files), respectively.
  \item \texttt{doc}: contains brief documentation notes.
  \item \texttt{eesupp}: contains the execution environment source code.
    Also subdivided into two subdirectories \texttt{inc} and
    \texttt{src}.
- \item \texttt{exe}: this directory is initially empty. It is the
-   default directory in which to execute the code.
  \item \texttt{model}: this directory contains the main source code.
    Also subdivided into two subdirectories \texttt{inc} and
    \texttt{src}.
-Line 311 
 structure).
+Line 278 
 structure).
    package corresponds to a subdirectory. For example, \texttt{gmredi}
    contains the code related to the Gent-McWilliams/Redi scheme,
    \texttt{aim} the code relative to the atmospheric intermediate
-   physics. The packages are described in detail in section 3.
+   physics. The packages are described in detail in chapter \ref{chap.packagesI}.
  \item \texttt{tools}: this directory contains various useful tools.
    For example, \texttt{genmake2} is a script written in csh (C-shell)
    that should be used to generate your makefile. The directory
    \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.
+   The latter is described in detail in part \ref{chap.ecco}.
+   This directory also contains the subdirectory build\_options, which
+   contains the `optfiles' with the compiler options for the different
+   compilers and machines that can run MITgcm.
  \item \texttt{utils}: this directory contains various utilities. The
    subdirectory \texttt{knudsen2} contains code and a makefile that
-Line 327 
 structure).
+Line 297 
 structure).
    \texttt{matlab} subdirectory contains matlab scripts for reading
    model output directly into matlab. \texttt{scripts} contains C-shell
    post-processing scripts for joining processor-based and tiled-based
-   model output.
+   model output. The subdirectory exch2 contains the code needed for
+   the exch2 package to work with different combinations of domain
+   decompositions.
  \item \texttt{verification}: this directory contains the model
    examples. See section \ref{sect:modelExamples}.
- \end{itemize}
+ \item \texttt{jobs}: contains sample job scripts for running MITgcm.
- \section[MITgcm Example Experiments]{Example experiments}
- \label{sect:modelExamples}
- \begin{rawhtml}
- <!-- CMIREDIR:modelExamples: -->
- \end{rawhtml}
- %% a set of twenty-four pre-configured numerical experiments
- The full MITgcm distribution comes with more than a dozen
- pre-configured numerical experiments. Some of these example
- experiments are tests of individual parts of the model code, but many
- are fully fledged numerical simulations. A few of the examples are
- used for tutorial documentation in sections \ref{sect:eg-baro} -
- \ref{sect:eg-global}.  The other examples follow the same general
- structure as the tutorial examples. However, they only include brief
- instructions in a text file called {\it README}.  The examples are
- located in subdirectories under the directory \texttt{verification}.
- Each example is briefly described below.
- \subsection{Full list of model examples}
- \begin{enumerate}
- \item \texttt{exp0} - single layer, ocean double gyre (barotropic with
-   free-surface). This experiment is described in detail in section
-   \ref{sect:eg-baro}.
- \item \texttt{exp1} - Four layer, ocean double gyre. This experiment
-   is described in detail in section \ref{sect:eg-baroc}.
- \item \texttt{exp2} - 4x4 degree global ocean simulation with steady
-   climatological forcing. This experiment is described in detail in
-   section \ref{sect:eg-global}.
- \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
-   channel with open boundaries.
- \item \texttt{exp5} - Inhomogenously forced ocean convection in a
-   doubly periodic box.
- \item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for
- Gent/McWilliams scheme). 2D (Y-Z).
- \item \texttt{internal wave} - Ocean internal wave forced by open
-   boundary conditions.
- \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
-   scheme; 1 month integration
- \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and
-   Suarez '94 forcing.
- \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and
-   Suarez '94 forcing.
- \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
-   Suarez '94 forcing on the cubed sphere.
- \item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
-   Global Zonal Mean configuration, 1x64x5 resolution.
- \item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
-   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).
- \item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
-   physics. 3D Equatorial Channel configuration.
- \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics.
-   Global configuration, on latitude longitude grid with 128x64x5 grid
-   points ($2.8^\circ$ resolution).
- \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on
-   latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
- \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on
-   cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
-   resolution).
- \item \texttt{advect\_cs} Two-dimensional passive advection test on
-   cube sphere grid.
- \item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive
-   advection test on Cartesian grid.
- \item \texttt{advect\_yz} Two-dimensional (vertical plane) passive
-   advection test on Cartesian grid.
- \item \texttt{carbon} Simple passive tracer experiment. Includes
-   derivative calculation. Described in detail in section
-   \ref{sect:eg-carbon-ad}.
- \item \texttt{flt\_example} Example of using float package.
- \item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux
-   boundary conditions and poles.
- \item \texttt{global\_ocean\_pressure} Global circulation in pressure
-   coordinate (non-Boussinesq ocean model). Described in detail in
-   section \ref{sect:eg-globalpressure}.
- \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
-   sphere grid.
- \end{enumerate}
- \subsection{Directory structure of model examples}
- Each example directory has the following subdirectories:
- \begin{itemize}
- \item \texttt{code}: contains the code particular to the example. At a
-   minimum, this directory includes the following files:
-   \begin{itemize}
-   \item \texttt{code/packages.conf}: declares the list of packages or
-     package groups to be used.  If not included, the default version
-     is located in \texttt{pkg/pkg\_default}.  Package groups are
-     simply convenient collections of commonly used packages which are
-     defined in \texttt{pkg/pkg\_default}.  Some packages may require
-     other packages or may require their absence (that is, they are
-     incompatible) and these package dependencies are listed in
-     \texttt{pkg/pkg\_depend}.
-   \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
-     the ``execution environment'' part of the code. The default
-     version is located in \texttt{eesupp/inc}.
-   \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to
-     the ``numerical model'' part of the code. The default version is
-     located in \texttt{model/inc}.
-   \item \texttt{code/SIZE.h}: declares size of underlying
-     computational grid.  The default version is located in
-     \texttt{model/inc}.
-   \end{itemize}
-   In addition, other include files and subroutines might be present in
-   \texttt{code} depending on the particular experiment. See Section 2
-   for more details.
- \item \texttt{input}: contains the input data files required to run
-   the example. At a minimum, the \texttt{input} directory contains the
-   following files:
-   \begin{itemize}
-   \item \texttt{input/data}: this file, written as a namelist,
-     specifies the main parameters for the experiment.
-   \item \texttt{input/data.pkg}: contains parameters relative to the
+ \item \texttt{lsopt}: Line search code used for optimization.
-     packages used in the experiment.
-   \item \texttt{input/eedata}: this file contains ``execution
+ \item \texttt{optim}: Interface between MITgcm and line search code.
-     environment'' data. At present, this consists of a specification
-     of the number of threads to use in $X$ and $Y$ under multithreaded
-     execution.
-   \end{itemize}
-   In addition, you will also find in this directory the forcing and
-   topography files as well as the files describing the initial state
-   of the experiment.  This varies from experiment to experiment. See
-   section 2 for more details.
- \item \texttt{results}: this directory contains the output file
-   \texttt{output.txt} produced by the simulation example. This file is
-   useful for comparison with your own output when you run the
-   experiment.
  \end{itemize}
- Once you have chosen the example you want to run, you are ready to
- compile the code.
  \section[Building MITgcm]{Building the code}
  \label{sect:buildingCode}
  \begin{rawhtml}
-Line 1087 
 as the pickup files but are named differ
+Line 894 
 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{MNC output files}
  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
  is usually (though not necessarily) placed within a subdirectory with
- a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files
+ a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.
- 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 \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} and it converts the netCDF
-   binaries into formatted ASCII text files.
- \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}
- http://meteora.ucsd.edu/~pierce/ncview_home_page.html
- \end{verbatim}
-   \begin{rawhtml} </A> \end{rawhtml}
- \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}
  \subsection{Looking at the output}
-Line 1163 
 Some examples of reading and visualizing
+Line 934 
 Some examples of reading and visualizing
  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
  they are described in Section \ref{sec:pkg:mnc}.
+ The MNC output files are all in the ``self-describing'' netCDF
+ format and can thus be browsed and/or plotted using tools such as:
+ \begin{itemize}
+ \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} and it converts the netCDF
+   binaries into formatted ASCII text files.
+ \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}
+ http://meteora.ucsd.edu/~pierce/ncview_home_page.html
+ \end{verbatim}
+   \begin{rawhtml} </A> \end{rawhtml}
+ \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}

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