--- manual/s_phys_pkgs/text/exch2.tex	2004/02/17 21:58:56	1.8
+++ manual/s_phys_pkgs/text/exch2.tex	2004/03/15 22:39:28	1.11
@@ -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 1.11 2004/03/15 22:39:28 afe Exp $
 % $Name:  $
 
 %%  * Introduction
@@ -10,31 +10,159 @@
 %%    o automatically inserted at \section{Reference} 
 
 
-\section{Extended Cubed Sphere Exchange}
+\section{exch2: Extended Cubed Sphere \mbox{Topology}}
 \label{sec:exch2}
 
 
 \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 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}, 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 \file{SIZE.h} file as
+detailed below.  Both files are generated by Matlab scripts in
+\file{utils/exch2/matlab-topology-generator}; see Section
+\ref{sec:topogen} \sectiontitle{Generating Topology Files for exch2}
+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$32 grid points, all
+running on a single processor.  Pregenerated examples of these files
+with alternate topologies are provided under
+\file{utils/exch2/code-mods} along with the appropriate \file{SIZE.h}
+file for single-processor execution.
+
+\subsection{Invoking exch2}
+
+To use exch2 with the cubed sphere, the following conditions must be
+met: \\
+
+$\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. \\
+
+$\bullet$ An example of \file{W2\_EXCH2\_TOPOLOGY.h} and
+  \file{w2\_e2setup.F} must reside in a directory containing code
+  linked when \file{genmake2} runs.  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
+  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
+  \file{tile???.mitgrid} where \file{???} is \file{001} through
+  \file{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 \file{SIZE.h}
+  must be placed where \file{genmake2} will find it.  In particular
+  for the 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}; a more general background on the subject
+  relvant to MITgcm is presented in Section
+  \ref{sect:specifying_a_decomposition}\sectiontitle{Specifying a
+  decomposition}.\\
+
+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 for exch2}
+\label{sec:topogen}
+
+Alternate cubed sphere topologies may be created using the Matlab
+scripts in \file{utils/exch2/matlab-topology-generator}. Running the
+m-file \file{driver.m} from the Matlab prompt (there are no parameters
+to pass) generates exch2 topology files \file{W2\_EXCH2\_TOPOLOGY.h}
+and \file{w2\_e2setup.F} in the working directory and displays a
+figure of the topology via Matlab.  The other m-files in the directory
+are subroutines of \file{driver.m} and should not be run except for
+development purposes. \\
+
+The parameters that determine the dimensions and topology of the
+generated configuration are \code{nr}, \code{nb}, \code{ng},
+\code{tnx} and \code{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 \code{tnx} and \code{tny} determine the dimensions of
+the tiles into which the subdomains are decomposed, and must evenly
+divide the integer assigned to \code{nr}, \code{nb} and \code{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$32 grid and
+twenty-four tiles (\code{tnx=16, tny=16})
+} \label{fig:24tile}
+\end{figure}
+
+\begin{figure}
+\begin{center}
+ \resizebox{4in}{!}{
+  \includegraphics{part6/s12t_16x32.ps}
+ }
+\end{center} 
+\caption{Plot of cubed sphere topology with a 32$\times$32 grid and
+twelve tiles (\code{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 otuning is useful in
+ocean modeling for omitting tiles that fall entirely on land.  The
+tiles omitted are specified in the file \file{blanklist.txt} by
+their tile number in the topology, separated by a newline. \\
+
+
+
+
+
 
 \subsection{Key Variables}
 
@@ -52,7 +180,7 @@
 \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