Diff of /manual/s_phys_pkgs/text/exch2.tex

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--- manual/s_phys_pkgs/text/exch2.tex	2005/07/18 20:45:27	1.24
+++ manual/s_phys_pkgs/text/exch2.tex	2005/08/09 21:52:09	1.25
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.24 2005/07/18 20:45:27 molod Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.25 2005/08/09 21:52:09 edhill Exp $
 % $Name:  $
 
 %%  * Introduction
@@ -23,7 +23,7 @@
 dimensions of the subdomain.  Furthermore, the tiles can run on
 separate processors individually or in groups, which provides for
 manual compile-time load balancing across a relatively arbitrary
-number of processors. \\
+number of processors.
 
 The exchange parameters are declared in
 \filelink{pkg/exch2/W2\_EXCH2\_TOPOLOGY.h}{pkg-exch2-W2_EXCH2_TOPOLOGY.h}
@@ -44,43 +44,46 @@
 \subsubsection{Invoking exch2}
 
 To use exch2 with the cubed sphere, the following conditions must be
-met: \\
+met:
 
-$\bullet$ 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. \\
+\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{packages.conf} file -- see Section \ref{sect:buildingCode}
+  \sectiontitle{Building the code} for general
+  details.
 
-$\bullet$ An example of \file{W2\_EXCH2\_TOPOLOGY.h} and
+\item 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.\\
-
-$\bullet$ 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
+  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 MITgcm support 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
   \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}.\\
+  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}
 
 At the time of this writing the following examples use exch2 and may
 be used for guidance:
@@ -188,21 +191,20 @@
 Once the topology configuration files are created, the Fortran
 \code{PARAMETER}s in \file{SIZE.h} must be configured to match.
 Section \ref{sect:specifying_a_decomposition} \sectiontitle{Specifying
-a decomposition} provides a general description of domain
+  a decomposition} provides a general description of domain
 decomposition within MITgcm and its relation to \file{SIZE.h}. The
-current section specifies constraints that the exch2 package
-imposes and describes how to enable parallel execution with
-MPI. \\
+current section specifies constraints that the exch2 package imposes
+and describes how to enable parallel execution with MPI.
 
 As in the general case, the parameters \varlink{sNx}{sNx} and
 \varlink{sNy}{sNy} define the size of the individual tiles, and so
 must be assigned the same respective values as \code{tnx} and
-\code{tny} in \file{driver.m}.\\
+\code{tny} in \file{driver.m}.
 
 The halo width parameters \varlink{OLx}{OLx} and \varlink{OLy}{OLy}
 have no special bearing on exch2 and may be assigned as in the general
-case. The same holds for \varlink{Nr}{Nr}, the number of vertical 
-levels in the model.\\
+case. The same holds for \varlink{Nr}{Nr}, the number of vertical
+levels in the model.
 
 The parameters \varlink{nSx}{nSx}, \varlink{nSy}{nSy},
 \varlink{nPx}{nPx}, and \varlink{nPy}{nPy} relate to the number of
@@ -210,7 +212,7 @@
 the tiles are stored in the $x$ dimension, and so
 \code{\varlink{nSy}{nSy}=1} in all cases.  Since the tiles as
 configured by exch2 cannot be split up accross processors without
-regenerating the topology, \code{\varlink{nPy}{nPy}=1} as well. \\
+regenerating the topology, \code{\varlink{nPy}{nPy}=1} as well.
 
 The number of tiles MITgcm allocates and how they are distributed
 between processors depends on \varlink{nPx}{nPx} and
@@ -227,12 +229,11 @@
 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}.\\
-
+\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 
-one processor: \\
+configuration illustrated in figure \ref{fig:12tile} running on one
+processor:
 
 \begin{verbatim}
       PARAMETER (
@@ -268,9 +269,6 @@
 \end{verbatim}
 
 
-
-
-
 \subsubsection{Key Variables}
 
 The descriptions of the variables are divided up into scalars,