--- manual/s_phys_pkgs/text/exch2.tex	2004/03/12 20:58:19	1.9
+++ manual/s_phys_pkgs/text/exch2.tex	2004/03/15 20:11:56	1.10
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.9 2004/03/12 20:58:19 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.10 2004/03/15 20:11:56 afe Exp $
 % $Name:  $
 
 %%  * Introduction
@@ -10,7 +10,7 @@
 %%    o automatically inserted at \section{Reference} 
 
 
-\section{Extended Cubed Sphere Exchange}
+\section{exch2: Extended Cubed Sphere \mbox{Topology}}
 \label{sec:exch2}
 
 
@@ -24,47 +24,64 @@
 individual tiles may be run on separate processors in different
 combinations, and whether exchanges between particular tiles occur
 between different processors is determined at runtime.  This
-flexibility provides for manual load balancing across a relatively
-arbitrary number of processors.
+flexibility provides for manual compile-time load balancing across a
+relatively arbitrary number of processors. \\
 
 The exchange parameters are declared in
 \filelink{pkg/exch2/W2\_EXCH2\_TOPOLOGY.h}{pkg-exch2-W2_EXCH2_TOPOLOGY.h}
 and assigned in
 \filelink{pkg/exch2/w2\_e2setup.F}{pkg-exch2-w2_e2setup.F}. The
 validity of the cube topology depends on the \texttt{SIZE.h} file as
-detailed below.  Both files are generated by Matlab scripts in ??
-check these in already! and should not be edited.  The default files
-provided in the release configure a cubed sphere arrangement of six
-tiles, one per subdomain, each with 32$\times$32 grid points, all
-running on a single processor.  Pregenerated examples of these files 
-with alternate topologies are provided in ??.
+detailed below.  Both files are generated by Matlab scripts in
+\texttt{utils/exch2/matlab-topology-generator}; see Section
+\ref{sec:topogen} for details on creating alternate topologies.  The
+default files provided in the release configure a cubed sphere
+topology of six tiles, one per subdomain, each with 32$\times$32 grid
+points, all running on a single processor.  Pregenerated examples of
+these files with alternate topologies are provided under
+\texttt{utils/exch2/code-mods} along with the appropriate
+\texttt{SIZE.h} file for single-processor execution.
 
 \subsection{Invoking exch2}
 
-To use exch2 with the cubed sphere, the following conditions must be met:
+To use exch2 with the cubed sphere, the following conditions must be
+met: \\
 
-- the exch2 package is included when \texttt{genmake2} is run.  The
+$\bullet$ The exch2 package is included when \texttt{genmake2} is run.  The
   easiest way to do this is to add the line \texttt{exch2} to the
   \texttt{profile.conf} file -- see Section \ref{sect:buildingCode}
   for general details. \\
 
-- an example of \texttt{W2\_EXCH2\_TOPOLOGY.h} and
+$\bullet$ An example of \texttt{W2\_EXCH2\_TOPOLOGY.h} and
   \texttt{w2\_e2setup.F} must reside in a directory containing code
   linked when \texttt{genmake2} runs.  The safest place to put these
   is the directory indicated in the \texttt{-mods=DIR} command line
   modifier (typically \texttt{../code}), or the build directory.  The
-  default versions of these files reside in \texttt{pkg/exch2}, but
-  they should be left untouched to avoid breaking configurations other
-  than the one you intend to modify.\\
-
-- files containing grid parameters, named
-  \texttt{tile}xxx\texttt{.mitgrid} where xxx is \texttt{001} through
-  \texttt{006}, must be in the working directory when the MITgcm
-  executable is run.  These files are provided in the example
-  experiments for cubed sphere configurations with 32$\times$32 cube
-  sides and are non-trivial to generate -- please contact MITgcm
-  support if you want to generate files for other configurations.
-  This is lame. ?? \\
+  default versions of these files reside in \texttt{pkg/exch2} and are
+  linked automatically if no other versions exist elsewhere in the
+  link path, but they should be left untouched to avoid breaking
+  configurations other than the one you intend to modify.\\
+
+$\bullet$ Files containing grid parameters, named
+  \texttt{tile}???\texttt{.mitgrid} where ??? is \texttt{001} through
+  \texttt{006} (one per subdomain), must be in the working directory
+  when the MITgcm executable is run.  These files are provided in the
+  example experiments for cubed sphere configurations with
+  32$\times$32 cube sides and are non-trivial to generate -- please
+  contact MITgcm support if you want to generate files for other
+  configurations. \\
+
+$\bullet$ As always when compiling MITgcm, the file \texttt{SIZE.h}
+  must be placed where \texttt{genmake2} will find it.  In particular
+  for the exch2, the domain decompositin specified in \texttt{SIZE.h}
+  must correspond with the particular configuration's topology
+  specified in \texttt{W2\_EXCH2\_TOPOLOGY.h} and
+  \texttt{w2\_e2setup.F}.  Domain decomposition issues particular to
+  exch2 are addressed in Section \ref{sec:topogen}: ``Generating
+  Topology Files for exch2''; a more general background on the subject
+  relvant to MITgcm is presented in Section
+  \ref{sect:specifying_a_decomposition}: ``Specifying a
+  decomposition''.\\
 
 As of the time of writing the following examples use exch2 and may be
 used for guidance:
@@ -80,7 +97,70 @@
 
 
 
-\subsection{Generating Topology Files}
+\subsection{Generating Topology Files for exch2}
+\label{sec:topogen}
+
+Alternate cubed sphere topologies may be created using the Matlab
+scripts in \texttt{utils/exch2/matlab-topology-generator}. Running the
+m-file \texttt{driver} from the Matlab prompt (without passing any
+function parameters) generates exch2 topology files
+\texttt{W2\_EXCH2\_TOPOLOGY.h} and \texttt{w2\_e2setup.F} in the
+working directory and displays via Matlab a figure of the topology.
+The other m-files in the directory are subroutines of \texttt{driver}
+and should not be run except for development purposes. \\
+
+The parameters that determine the dimensions and topology of the
+generated configuration are nr, nb, ng, tnx and tny, and all are
+assigned early in the script.
+
+The first three determine the size of the subdomains (cube faces) and
+hence the size of the overall domain.  Each one determines the number
+of grid points, and therefore the resolution, along the subdomain
+sides in a ``great circle'' around each axis of the cube.  At the time
+of this writing MITgcm requires these three parameters to be equal,
+but they provide for future releases of MITgcm to accomodate different
+resolutions around the axes to allow (for example) greater resolution
+around the equator.\\
+
+The parameters tnx and tny determine the dimensions of the tiles into
+which the subdomains are decomposed, and must evenly divide the
+integer assigned to nr, nb and ng.  The result is a rectangular tiling
+of the subdomain.  Figure \ref{fig:24tile} shows one possible topology
+for a twenty-four tile cube, and figure \ref{fig:12tile} shows one for
+twelve tiles. \\
+
+\begin{figure}
+\begin{center}
+ \resizebox{4in}{!}{
+  \includegraphics{part6/s24t_16x16.ps}
+ }
+\end{center} 
+\caption{Plot of cubed sphere topology with a 32$\times$32 grid and
+twenty-four tiles (tnx=16, tny=16)
+} \label{fig:24tile}
+\end{figure}
+
+\begin{figure}
+\begin{center}
+ \resizebox{4in}{!}{
+  \includegraphics{part6/s12t_16x32.ps}
+ }
+\end{center} 
+\caption{Plot of cubed sphere topology with a 32$\times$32 grid and
+twelve tiles (tnx=16, tny=32)
+} \label{fig:12tile}
+\end{figure}
+
+Tiles can be selected from the topology to be omitted from being
+allocated memory and processors.  This kind of tuning is useful in
+ocean modeling for omitting tiles that fall entirely on land.  The
+tiles omitted are specified in the file \texttt{blanklist.txt} by
+their tile number in the topology, separated by a newline. \\
+
+
+
+
+
 
 \subsection{Key Variables}