--- manual/s_getstarted/text/getting_started.tex	2006/06/28 17:20:51	1.38
+++ manual/s_getstarted/text/getting_started.tex	2010/08/30 23:09:20	1.44
@@ -1,22 +1,20 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.38 2006/06/28 17:20:51 molod Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.44 2010/08/30 23:09:20 jmc Exp $
 % $Name:  $
 
 %\section{Getting started}
 
-In this section, we describe how to use the model. In the first
-section, we provide enough information to help you get started with
-the model. We believe the best way to familiarize yourself with the
+We believe the best way to familiarize yourself with the
 model is to run the case study examples provided with the base
 version. Information on how to obtain, compile, and run the code is
-found there as well as a brief description of the model structure
-directory and the case study examples.  The latter and the code
-structure are described more fully in chapters
-\ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in
-this section, we provide information on how to customize the code when
-you are ready to try implementing the configuration you have in mind.
+found here as well as a brief description of the model structure
+directory and the case study examples. Information is also provided
+here on how to customize the code when you are ready to try implementing 
+the configuration you have in mind.  The code and algorithm
+are described more fully in chapters \ref{chap:discretization} and 
+\ref{chap:sarch}. 
 
 \section{Where to find information}
-\label{sect:whereToFindInfo}
+\label{sec:whereToFindInfo}
 \begin{rawhtml}
 <!-- CMIREDIR:whereToFindInfo: -->
 \end{rawhtml}
@@ -31,7 +29,7 @@
 \begin{rawhtml} </A> \end{rawhtml}
 
 \section{Obtaining the code}
-\label{sect:obtainingCode}
+\label{sec:obtainingCode}
 \begin{rawhtml}
 <!-- CMIREDIR:obtainingCode: -->
 \end{rawhtml}
@@ -65,7 +63,7 @@
 \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
@@ -104,9 +102,9 @@
 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}
 
@@ -141,7 +139,7 @@
 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/public/using_cvs.html" target="idontexist"> \end{rawhtml}
 here
 \begin{rawhtml} </A> \end{rawhtml} 
 .
@@ -221,11 +219,11 @@
 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:
-\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/download/
 \end{verbatim}
@@ -278,7 +276,7 @@
   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)
@@ -302,7 +300,7 @@
   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.
   
@@ -313,7 +311,7 @@
 \end{itemize}
 
 \section[Building MITgcm]{Building the code}
-\label{sect:buildingCode}
+\label{sec:buildingCode}
 \begin{rawhtml}
 <!-- CMIREDIR:buildingCode: -->
 \end{rawhtml}
@@ -322,7 +320,7 @@
 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.
 
@@ -397,7 +395,7 @@
 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/* .
@@ -411,7 +409,7 @@
 
 \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
@@ -515,16 +513,30 @@
 
 
 \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.
 \texttt{genmake2} is a shell script written to work with all
 ``sh''--compatible shells including bash v1, bash v2, and Bourne.
-Internally, \texttt{genmake2} determines the locations of needed
-files, the compiler, compiler options, libraries, and Unix tools.  It
-relies upon a number of ``optfiles'' located in the
-\texttt{tools/build\_options} directory.
+%Internally, \texttt{genmake2} determines the locations of needed
+%files, the compiler, compiler options, libraries, and Unix tools.  It
+%relies upon a number of ``optfiles'' located in the
+%\texttt{tools/build\_options} directory.
+\texttt{genmake2} parses information from the following sources:
+\begin{description}
+\item[-] a {\em gemake\_local} file if one is found in the current 
+  directory
+\item[-] command-line options
+\item[-] an "options file" as specified by the command-line option
+  \texttt{--optfile=/PATH/FILENAME}
+\item[-] a {\em packages.conf} file (if one is found) with the 
+  specific list of packages to compile. The search path for 
+  file {\em packages.conf} is, first, the current directory and
+  then each of the "MODS" directories in the given order (see below).
+\end{description}
+
+\subsubsection{Optfiles in \texttt{tools/build\_options} directory:}
 
 The purpose of the optfiles is to provide all the compilation options
 for particular ``platforms'' (where ``platform'' roughly means the
@@ -597,6 +609,8 @@
 \begin{rawhtml} </A> \end{rawhtml}
 mailing list.
 
+\subsubsection{Command-line options:}
+
 In addition to the optfiles, \texttt{genmake2} supports a number of
 helpful command-line options.  A complete list of these options can be
 obtained from:
@@ -619,21 +633,31 @@
   the user's path.  When these three items have been identified,
   genmake2 will try to find an optfile that has a matching name.
   
-\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
-  set of packages to be used.  The normal order of precedence for
-  packages is as follows:
-  \begin{enumerate}
-  \item If available, the command line (\texttt{--pdefault}) settings
-    over-rule any others.
-
-  \item Next, \texttt{genmake2} will look for a file named
-    ``\texttt{packages.conf}'' in the local directory or in any of the
-    directories specified with the \texttt{--mods} option.
-    
-  \item Finally, if neither of the above are available,
-    \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
-  \end{enumerate}
+\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
+  directories containing ``modifications''.  These directories contain
+  files with names that may (or may not) exist in the main MITgcm
+  source tree but will be overridden by any identically-named sources
+  within the ``MODS'' directories.
   
+  The order of precedence for this "name-hiding" is as follows:
+  \begin{itemize}
+  \item ``MODS'' directories (in the order given)
+  \item Packages either explicitly specified or provided by default
+    (in the order given)
+  \item Packages included due to package dependencies (in the order
+    that that package dependencies are parsed)
+  \item The "standard dirs" (which may have been specified by the
+    ``-standarddirs'' option)
+  \end{itemize}
+  
+\item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
+  where package groups are defined. If not set, the package-groups 
+  definition will be read from {\em pkg/pkg\_groups}.
+  It also contains the default list of packages (defined
+  as the group ``{\it default\_pkg\_list}'' which is used
+  when no specific package list ({\em packages.conf})
+  is found in current directory or in any "MODS" directory.
+
 \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
   used for packages.
   
@@ -658,26 +682,9 @@
   "STAF" compiler.  As with any compilers, it is helpful to have their
   directories listed in your {\tt \$PATH} environment variable.
   
-\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
-  directories containing ``modifications''.  These directories contain
-  files with names that may (or may not) exist in the main MITgcm
-  source tree but will be overridden by any identically-named sources
-  within the ``MODS'' directories.
-  
-  The order of precedence for this "name-hiding" is as follows:
-  \begin{itemize}
-  \item ``MODS'' directories (in the order given)
-  \item Packages either explicitly specified or provided by default
-    (in the order given)
-  \item Packages included due to package dependencies (in the order
-    that that package dependencies are parsed)
-  \item The "standard dirs" (which may have been specified by the
-    ``-standarddirs'' option)
-  \end{itemize}
-  
 \item[\texttt{--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
@@ -700,7 +707,7 @@
 
 
 \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
@@ -715,9 +722,9 @@
   
 \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/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">
+    href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
   \end{rawhtml}
   \begin{center}
     \texttt{MITgcm/tools/build\_options/}
@@ -750,7 +757,7 @@
   \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
@@ -768,14 +775,21 @@
   library and a job scheduling and queueing system such as PBS,
   LoadLeveller, Condor, or any of a number of similar tools.  A few
   example scripts (those used for our \begin{rawhtml} <A
-    href="http://mitgcm.org/testing.html"> \end{rawhtml}regular
+    href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
   verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
   at:
   \begin{rawhtml} <A
-    href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
+    href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/">
+  \end{rawhtml}
+  {\footnotesize \tt
+    http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
+  \begin{rawhtml} </A> \end{rawhtml}
+  or at:
+  \begin{rawhtml} <A
+    href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
   \end{rawhtml}
   {\footnotesize \tt
-    http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }
+    http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
   \begin{rawhtml} </A> \end{rawhtml}
 
 \end{enumerate}
@@ -797,12 +811,12 @@
 \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.
 
