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

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-revision 1.42 by jmc,
Fri May 28 02:09:59 2010 UTC
+revision 1.44 by jmc,
Mon Aug 30 23:09:20 2010 UTC
 Line 14 
 are described more fully in chapters \re
  \ref{chap:sarch}.
  \section{Where to find information}
- \label{sect:whereToFindInfo}
+ \label{sec:whereToFindInfo}
  \begin{rawhtml}
  <!-- CMIREDIR:whereToFindInfo: -->
  \end{rawhtml}
 Line 29 
 http://mitgcm.org/pipermail/mitgcm-suppo
  \begin{rawhtml} </A> \end{rawhtml}
  \section{Obtaining the code}
- \label{sect:obtainingCode}
+ \label{sec:obtainingCode}
  \begin{rawhtml}
  <!-- CMIREDIR:obtainingCode: -->
  \end{rawhtml}
 Line 63 
 provide easy support for maintenance upd
  \end{enumerate}
  \subsection{Method 1 - Checkout from CVS}
- \label{sect:cvs_checkout}
+ \label{sec:cvs_checkout}
  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
 Line 102 
 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/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
  \begin{verbatim}
- http://mitgcm.org/source_code.html
+ http://mitgcm.org/viewvc/MITgcm/MITgcm/
  \end{verbatim}
  \begin{rawhtml} </A> \end{rawhtml}
-Line 220 
 also means we can't tell what version of
+Line 219 
 also means we can't tell what version of
  with. So please be sure you understand what you're doing.
  \subsection{Method 2 - Tar file download}
- \label{sect:conventionalDownload}
+ \label{sec:conventionalDownload}
  If you do not have CVS on your system, you can download the model as a
  tar file from the web site at:
-Line 277 
 structure).
+Line 276 
 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 chapter \ref{chap.packagesI}.
+   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)
-Line 301 
 structure).
+Line 300 
 structure).
    decompositions.
  \item \texttt{verification}: this directory contains the model
-   examples. See section \ref{sect:modelExamples}.
+   examples. See section \ref{sec:modelExamples}.
  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
-Line 312 
 structure).
+Line 311 
 structure).
  \end{itemize}
  \section[Building MITgcm]{Building the code}
- \label{sect:buildingCode}
+ \label{sec:buildingCode}
  \begin{rawhtml}
  <!-- CMIREDIR:buildingCode: -->
  \end{rawhtml}
-Line 321 
 To compile the code, we use the \texttt{
+Line 320 
 To compile the code, we use the \texttt{
  file (\texttt{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 (\texttt{genmake2}), described
- in section \ref{sect:genmake}, that automatically creates the
+ in section \ref{sec:genmake}, that automatically creates the
  \texttt{Makefile} for you. You then need to build the dependencies and
  compile the code.
-Line 396 
 where the ``2'' can be replaced with a n
+Line 395 
 where the ``2'' can be replaced with a n
  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 by
+ given in section \ref{sec:runModel}. Here, we can run the model by
  first creating links to all the input files:
  \begin{verbatim}
  ln -s ../input/* .
-Line 410 
 where we are re-directing the stream of
+Line 409 
 where we are re-directing the stream of
  \subsection{Building/compiling the code elsewhere}
- In the example above (section \ref{sect:buildingCode}) we built the
+ In the example above (section \ref{sec: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
-Line 514 
 the one experiment:
+Line 513 
 the one experiment:
  \subsection{Using \texttt{genmake2}}
- \label{sect:genmake}
+ \label{sec:genmake}
  To compile the code, first use the program \texttt{genmake2} (located
  in the \texttt{tools} directory) to generate a Makefile.
-Line 685 
 The most important command-line options
+Line 684 
 The most important command-line options
  \item[\texttt{--mpi}] This option enables certain MPI features (using
    CPP \texttt{\#define}s) within the code and is necessary for MPI
-   builds (see Section \ref{sect:mpi-build}).
+   builds (see Section \ref{sec:mpi-build}).
  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
    soft-links and other bugs common with the \texttt{make} versions
-Line 708 
 The most important command-line options
+Line 707 
 The most important command-line options
  \subsection{Building with MPI}
- \label{sect:mpi-build}
+ \label{sec:mpi-build}
  Building MITgcm to use MPI libraries can be complicated due to the
  variety of different MPI implementations available, their dependencies
-Line 723 
 The steps for building MITgcm with MPI s
+Line 722 
 The steps for building MITgcm with MPI s
  \item Determine the locations of your MPI-enabled compiler and/or MPI
    libraries and put them into an options file as described in Section
-   \ref{sect:genmake}.  One can start with one of the examples in:
+   \ref{sec:genmake}.  One can start with one of the examples in:
    \begin{rawhtml} <A
      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
    \end{rawhtml}
-Line 758 
 The steps for building MITgcm with MPI s
+Line 757 
 The steps for building MITgcm with MPI s
    \end{itemize}
  \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
-   (see Section \ref{sect:genmake}) using commands such as:
+   (see Section \ref{sec:genmake}) using commands such as:
  {\footnotesize \begin{verbatim}
    %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
    %  make depend
-Line 812 
 the GNU g77 compiler and the mpich MPI l
+Line 811 
 the GNU g77 compiler and the mpich MPI l
  \end{verbatim} }
  \section[Running MITgcm]{Running the model in prognostic mode}
- \label{sect:runModel}
+ \label{sec:runModel}
  \begin{rawhtml}
  <!-- CMIREDIR:runModel: -->
  \end{rawhtml}
- If compilation finished succesfully (section \ref{sect:buildingCode})
+ If compilation finished succesfully (section \ref{sec:buildingCode})
  then an executable called \texttt{mitgcmuv} will now exist in the
  local directory.

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