--- manual/s_phys_pkgs/text/exch2.tex	2004/02/17 21:58:56	1.8
+++ manual/s_phys_pkgs/text/exch2.tex	2004/03/12 20:58:19	1.9
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.8 2004/02/17 21:58:56 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.9 2004/03/12 20:58:19 afe Exp $
 % $Name:  $
 
 %%  * Introduction
@@ -17,24 +17,70 @@
 \subsection{Introduction}
 
 The \texttt{exch2} package is an extension to the original cubed
-sphere exchanges to allow more flexible domain decomposition and
-parallelization.  Cube faces (subdomains) may be divided into whatever
-number of tiles that divide evenly into the grid point dimensions of
-the subdomain.  Furthermore, the 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.
+sphere topological configuration that allows more flexible domain
+decomposition and parallelization.  Cube faces (also called
+subdomains) may be divided into any number of tiles that divide evenly
+into the grid point dimensions of the subdomain.  Furthermore, the
+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.
 
 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}, both in
-the \texttt{pkg/exch2} directory.  The validity of the cube topology
-depends on the \texttt{SIZE.h} file as detailed below.  Both files are
-generated by Matlab scripts and should not be edited.  The default
-files provided in the release set up a cube sphere arrangement of six
-tiles, one per subdomain, each with 32x32 grid points, running on a
-single processor.
+\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$32 grid points, all
+running on a single processor.  Pregenerated examples of these files 
+with alternate topologies are provided in ??.
+
+\subsection{Invoking exch2}
+
+To use exch2 with the cubed sphere, the following conditions must be met:
+
+- the exch2 package is included when \texttt{genmake2} is run.  The
+  easiest way to do this is to add the line \texttt{exch2} to the
+  \texttt{profile.conf} file -- see Section \ref{sect:buildingCode}
+  for general details. \\
+
+- an example of \texttt{W2\_EXCH2\_TOPOLOGY.h} and
+  \texttt{w2\_e2setup.F} must reside in a directory containing code
+  linked when \texttt{genmake2} runs.  The safest place to put these
+  is the directory indicated in the \texttt{-mods=DIR} command line
+  modifier (typically \texttt{../code}), or the build directory.  The
+  default versions of these files reside in \texttt{pkg/exch2}, but
+  they should be left untouched to avoid breaking configurations other
+  than the one you intend to modify.\\
+
+- files containing grid parameters, named
+  \texttt{tile}xxx\texttt{.mitgrid} where xxx is \texttt{001} through
+  \texttt{006}, must be in the working directory when the MITgcm
+  executable is run.  These files are provided in the example
+  experiments for cubed sphere configurations with 32$\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. ?? \\
+
+As of the time of writing the following examples use exch2 and may be
+used for guidance:
+
+\begin{verbatim}
+verification/adjust_nlfs.cs-32x32x1
+verification/adjustment.cs-32x32x1 
+verification/aim.5l_cs
+verification/global_ocean.cs32x15
+verification/hs94.cs-32x32x5
+\end{verbatim}
+
+
+
+
+\subsection{Generating Topology Files}
 
 \subsection{Key Variables}
 
@@ -52,7 +98,7 @@
 \texttt{NTILES}, and the maximum number of neighbors of any tiles by
 \texttt{MAX\_NEIGHBOURS}.  These parameters are used for defining the
 size of the various one and two dimensional arrays that store tile
-parameters indexed to the tile number.
+parameters indexed to the tile number.\\
 
 The scalar parameters \varlink{exch2\_domain\_nxt}{exch2_domain_nxt}
 and \varlink{exch2\_domain\_nyt}{exch2_domain_nyt} express the number