--- manual/s_phys_pkgs/text/exch2.tex	2004/10/12 17:27:17	1.21
+++ manual/s_phys_pkgs/text/exch2.tex	2005/06/10 19:34:09	1.23
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.21 2004/10/12 17:27:17 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.23 2005/06/10 19:34:09 afe Exp $
 % $Name:  $
 
 %%  * Introduction
@@ -44,54 +44,43 @@
 \subsection{Invoking exch2}
 
 To use exch2 with the cubed sphere, the following conditions must be
-met:
+met: \\
 
-\begin{itemize}
-\item The exch2 package is included when \file{genmake2} is run.  The
-  easiest way to do this is to add the line \code{exch2} to the
-  \file{profile.conf} file -- see Section \ref{sect:buildingCode}
-  \sectiontitle{Building the code} for general details.
-  
-\item An example of \file{W2\_EXCH2\_TOPOLOGY.h} and
+$\bullet$ The exch2 package is included when \file{genmake2} is run.
+  The easiest way to do this is to add the line \code{exch2} to the
+  \file{profile.conf} file -- see Section
+  \ref{sect:buildingCode} \sectiontitle{Building the code} for general
+  details. \\
+
+$\bullet$ An example of \file{W2\_EXCH2\_TOPOLOGY.h} and
   \file{w2\_e2setup.F} must reside in a directory containing files
-  symbolically linked by the \file{genmake2} script.  The safest place
-  to put these is the directory indicated in the \code{-mods=DIR}
-  command line modifier (typically \file{../code}), or the build
-  directory.  The default versions of these files reside in
-  \file{pkg/exch2} and are linked automatically if no other versions
-  exist elsewhere in the build path, but they should be left untouched
-  to avoid breaking configurations other than the one you intend to
-  modify.
-  
-\item Files containing grid parameters, named \file{tile00$n$.mitgrid}
-  where $n$=\code{(1:6)} (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$32 cube sides -- please contact
-  \begin{rawhtml}
-    <A href="mailto:mitgcm-support@dev.mitgcm.org"> 
-  \end{rawhtml} 
-\begin{verbatim}
-MITgcm-support@mitgcm.org
-\end{verbatim}
-  \begin{rawhtml} </A> \end{rawhtml}
-  if you want to generate files for other configurations.
-  
-\item As always when compiling MITgcm, the file \file{SIZE.h} must be
-  placed where \file{genmake2} will find it.  In particular for exch2,
-  the domain decomposition specified in \file{SIZE.h} must correspond
-  with the particular configuration's topology specified in
+  symbolically linked by the \file{genmake2} script.  The safest place to
+  put these is the directory indicated in the \code{-mods=DIR} command
+  line modifier (typically \file{../code}), or the build directory.
+  The default versions of these files reside in \file{pkg/exch2} and
+  are linked automatically if no other versions exist elsewhere in the
+  build path, but they should be left untouched to avoid breaking
+  configurations other than the one you intend to modify.\\
+
+$\bullet$ Files containing grid parameters, named
+  \file{tile00$n$.mitgrid} where $n$=\code{(1:6)} (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$32 cube sides 
+  -- please contact MITgcm support if you want to generate
+  files for other configurations. \\
+
+$\bullet$ As always when compiling MITgcm, the file \file{SIZE.h} must
+  be placed where \file{genmake2} will find it.  In particular for
+  exch2, the domain decomposition specified in \file{SIZE.h} must
+  correspond with the particular configuration's topology specified in
   \file{W2\_EXCH2\_TOPOLOGY.h} and \file{w2\_e2setup.F}.  Domain
   decomposition issues particular to exch2 are addressed in Section
   \ref{sec:topogen} \sectiontitle{Generating Topology Files for exch2}
-  and \ref{sec:exch2mpi} \sectiontitle{exch2, SIZE.h, and
-    Multiprocessing}; a more general background on the subject
-  relevant to MITgcm is presented in Section
-  \ref{sect:specifying_a_decomposition} \sectiontitle{Specifying a
-    decomposition}.
-\end{itemize}
-
-
+  and \ref{sec:exch2mpi} \sectiontitle{exch2, SIZE.h, and Multiprocessing}; a more
+  general background on the subject relevant to MITgcm is presented in
+  Section \ref{sect:specifying_a_decomposition}
+  \sectiontitle{Specifying a decomposition}.\\
 
 At the time of this writing the following examples use exch2 and may
 be used for guidance:
@@ -226,12 +215,20 @@
 The number of tiles MITgcm allocates and how they are distributed
 between processors depends on \varlink{nPx}{nPx} and
 \varlink{nSx}{nSx}.  \varlink{nSx}{nSx} is the number of tiles per
-processor and \varlink{nPx}{nPx} is the number of processors.  The total
-number of tiles in the topology minus those listed in
-\file{blanklist.txt} must equal \code{nSx*nPx}.  Note that in order to 
+processor and \varlink{nPx}{nPx} is the number of processors.  The
+total number of tiles in the topology minus those listed in
+\file{blanklist.txt} must equal \code{nSx*nPx}.  Note that in order to
 obtain maximum usage from a given number of processors in some cases,
-this restriction might entail sharing a processor with a tile that would 
-otherwise be excluded. \\
+this restriction might entail sharing a processor with a tile that
+would otherwise be excluded because it is topographically outside of
+the domain and therefore in \file{blanklist.txt}.  For example,
+suppose you have five processors and a domain decomposition of
+thirty-six tiles that allows you to exclude seven tiles.  To evenly
+distribute the remaining twenty-nine tiles among five processors, you
+would have to run one ``dummy'' tile to make an even six tiles per
+processor.  Such dummy tiles are \emph{not} listed in
+\file{blanklist.txt}.\\
+
 
 The following is an example of \file{SIZE.h} for the twelve-tile
 configuration illustrated in figure \ref{fig:12tile} running on 
@@ -311,7 +308,7 @@
 
 The following arrays are of length \code{NTILES} and are indexed to
 the tile number, which is indicated in the diagrams with the notation
-\code{tn}.  The indices are omitted in the descriptions. \\
+\textsf{t}$n$.  The indices are omitted in the descriptions. \\
 
 The arrays \varlink{exch2\_tnx}{exch2_tnx} and
 \varlink{exch2\_tny}{exch2_tny} express the $x$ and $y$ dimensions of
@@ -339,11 +336,11 @@
 
 The array \varlink{exch2\_myFace}{exch2_myFace} contains the number of
 the subdomain of each tile, in a range \code{(1:6)} in the case of the
-standard cube topology and indicated by \textbf{\textsf{fn}} in
-figures \ref{fig:12tile} and \ref{fig:24tile}. The
-\varlink{exch2\_nNeighbours}{exch2_nNeighbours} variable contains a
-count of the neighboring tiles each tile has, and sets the bounds for
-looping over neighboring tiles.  And
+standard cube topology and indicated by \textbf{\textsf{f}}$n$ in
+figures \ref{fig:12tile} and
+\ref{fig:24tile}. \varlink{exch2\_nNeighbours}{exch2_nNeighbours}
+contains a count of the neighboring tiles each tile has, and sets 
+the bounds for looping over neighboring tiles.
 \varlink{exch2\_tProc}{exch2_tProc} holds the process rank of each
 tile, and is used in interprocess communication.  \\
 
