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-revision 1.22 by edhill,
Tue Oct 12 18:16:03 2004 UTC
+revision 1.28 by jmc,
Fri Aug 27 13:15:37 2010 UTC
 Line 10
  %%    o automatically inserted at \section{Reference}
- \section{exch2: Extended Cubed Sphere \mbox{Topology}}
+ \subsection{exch2: Extended Cubed Sphere \mbox{Topology}}
  \label{sec:exch2}
- \label{sec:pkg:exch2}
- \begin{rawhtml}
- <!-- CMIREDIR:package_exch2: -->
- \end{rawhtml}
- \subsection{Introduction}
+ \subsubsection{Introduction}
  The \texttt{exch2} package extends the original cubed sphere topology
  configuration to allow more flexible domain decomposition and
-Line 27 
 into any number of tiles that divide eve
+Line 23 
 into any number of tiles that divide eve
  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}
-Line 45 
 of these files with alternate topologies
+Line 41 
 of these files with alternate topologies
  \file{utils/exch2/code-mods} along with the appropriate \file{SIZE.h}
  file for single-processor execution.
- \subsection{Invoking exch2}
+ \subsubsection{Invoking exch2}
  To use exch2 with the cubed sphere, the following conditions must be
  met:
-Line 53 
 met:
+Line 49 
 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}
+   \file{packages.conf} file -- see Section \ref{sect:buildingCode}
-   \sectiontitle{Building the code} for general details.
+   \sectiontitle{Building the code} for general
+   details.
  \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
-Line 66 
 met:
+Line 63 
 met:
    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$32 cube sides -- please contact
+   with 32$\times$32 cube sides -- please contact MITgcm support if you
-   \begin{rawhtml}
+   want to generate files for other configurations.
-     <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
-Line 91 
 MITgcm-support@mitgcm.org
+Line 81 
 MITgcm-support@mitgcm.org
    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
+   \ref{sect:specifying_a_decomposition}
-     decomposition}.
+   \sectiontitle{Specifying a decomposition}.
  \end{itemize}
  At the time of this writing the following examples use exch2 and may
  be used for guidance:
-Line 111 
 verification/hs94.cs-32x32x5
+Line 99 
 verification/hs94.cs-32x32x5
- \subsection{Generating Topology Files for exch2}
+ \subsubsection{Generating Topology Files for exch2}
  \label{sec:topogen}
  Alternate cubed sphere topologies may be created using the Matlab
-Line 121 
 m-file
+Line 109 
 m-file
  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 -- figures \ref{fig:6tile}, \ref{fig:12tile},
+ the topology via Matlab -- figures \ref{fig:6tile}, \ref{fig:18tile},
- and \ref{fig:24tile} are examples of the generated diagrams.  The other
+ and \ref{fig:48tile} are examples of the generated diagrams.  The other
  m-files in the directory are
  subroutines called from \file{driver.m} and should not be run ``bare'' except
  for development purposes. \\
-Line 143 
 The parameters \code{tnx} and \code{tny}
+Line 131 
 The parameters \code{tnx} and \code{tny}
  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
+ \ref{fig:48tile} shows one possible topology for a twenty-four-tile
- cube, and figure \ref{fig:12tile} shows one for twelve tiles. \\
+ cube, and figure \ref{fig:6tile} shows one for six tiles. \\
  \begin{figure}
  \begin{center}
-  \resizebox{4in}{!}{
+  \resizebox{6in}{!}{
-   \includegraphics{part6/s24t_16x16.ps}
+ % \includegraphics{s_phys_pkgs/figs/s24t_16x16.ps}
+   \includegraphics{s_phys_pkgs/figs/adjust_cs.ps}
   }
  \end{center}
  \caption{Plot of a cubed sphere topology with a 32$\times$192 domain
  divided into six 32$\times$32 subdomains, each of which is divided
- into four tiles of width \code{tnx=16} and height \code{tny=16} for a
+ into eight tiles of width \code{tnx=16} and height \code{tny=8} for a
- total of twenty-four tiles.  The colored borders of the subdomains
+ total of forty-eight tiles. The colored borders of the subdomains
- represent the parameters \code{nr} (red), \code{nb} (blue), and
+ represent the parameters \code{nr} (red), \code{ng} (green), and
- \code{ng} (green).  } \label{fig:24tile}
+ \code{nb} (blue).
+ This tiling is used in the example
+ verification/adjustment.cs-32x32x1/
+ with the option (blanklist.txt) to remove the land-only 4 tiles
+ (11,12,13,14) which are filled in red on the plot.
+ } \label{fig:48tile}
  \end{figure}
  \begin{figure}
  \begin{center}
-  \resizebox{4in}{!}{
+  \resizebox{6in}{!}{
-   \includegraphics{part6/s12t_16x32.ps}
+ % \includegraphics{s_phys_pkgs/figs/s12t_16x32.ps}
+   \includegraphics{s_phys_pkgs/figs/polarcap.ps}
   }
  \end{center}
- \caption{Plot of a cubed sphere topology with a 32$\times$192 domain
+ \caption{Plot of a non-square cubed sphere topology with
- divided into six 32$\times$32 subdomains of two tiles each
+subdomains of different size (nr=90,ng=360,nb=90),
-  (\code{tnx=16, tny=32}).
+ divided into one to four tiles each
- } \label{fig:12tile}
+  (\code{tnx=90, tny=90}), resulting in a total of 18 tiles.
+ } \label{fig:18tile}
  \end{figure}
  \begin{figure}
  \begin{center}
   \resizebox{4in}{!}{
-   \includegraphics{part6/s6t_32x32.ps}
+ % \includegraphics{s_phys_pkgs/figs/s6t_32x32.ps}
+   \includegraphics{s_phys_pkgs/figs/s6t_32x32.ps}
   }
  \end{center}
  \caption{Plot of a cubed sphere topology with a 32$\times$192 domain
-Line 197 
 by their tile number in the topology, se
+Line 194 
 by their tile number in the topology, se
- \subsection{exch2, SIZE.h, and Multiprocessing}
+ \subsubsection{exch2, SIZE.h, and Multiprocessing}
  \label{sec:exch2mpi}
  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
+ current section specifies constraints that the exch2 package imposes
- imposes and describes how to enable parallel execution with
+ and describes how to enable parallel execution with MPI.
- 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.\\
+ levels in the model.
  The parameters \varlink{nSx}{nSx}, \varlink{nSy}{nSy},
  \varlink{nPx}{nPx}, and \varlink{nPy}{nPy} relate to the number of
-Line 225 
 tiles and how they are distributed on pr
+Line 221 
 tiles and how they are distributed on pr
  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
  \varlink{nSx}{nSx}.  \varlink{nSx}{nSx} is the number of tiles per
- processor and \varlink{nPx}{nPx} is the number of processors.  The total
+ processor and \varlink{nPx}{nPx} is the number of processors.  The
- number of tiles in the topology minus those listed in
+ 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
+ this restriction might entail sharing a processor with a tile that
- otherwise be excluded. \\
+ would otherwise be excluded because it is topographically outside of
+ the domain and therefore in \file{blanklist.txt}.  For example,
- The following is an example of \file{SIZE.h} for the twelve-tile
+ suppose you have five processors and a domain decomposition of
- configuration illustrated in figure \ref{fig:12tile} running on
+ thirty-six tiles that allows you to exclude seven tiles.  To evenly
- one processor: \\
+ 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 six-tile
+ configuration illustrated in figure \ref{fig:6tile}
+ running on one processor:
  \begin{verbatim}
        PARAMETER (
-      &           sNx =  16,
+      &           sNx =  32,
       &           sNy =  32,
       &           OLx =   2,
       &           OLy =   2,
-      &           nSx =  12,
+      &           nSx =   6,
       &           nSy =   1,
       &           nPx =   1,
       &           nPy =   1,
-Line 256 
 one processor: \\
+Line 259 
 one processor: \\
       &           Nr  =   5)
  \end{verbatim}
- The following is an example for the twenty-four-tile topology in
+ The following is an example for the forty-eight-tile topology in
- figure \ref{fig:24tile} running on six processors:
+ figure \ref{fig:48tile} running on six processors:
  \begin{verbatim}
        PARAMETER (
       &           sNx =  16,
-      &           sNy =  16,
+      &           sNy =   8,
       &           OLx =   2,
       &           OLy =   2,
-      &           nSx =   4,
+      &           nSx =   8,
       &           nSy =   1,
       &           nPx =   6,
       &           nPy =   1,
-Line 275 
 figure \ref{fig:24tile} running on six p
+Line 278 
 figure \ref{fig:24tile} running on six p
  \end{verbatim}
+ \subsubsection{Key Variables}
- \subsection{Key Variables}
  The descriptions of the variables are divided up into scalars,
  one-dimensional arrays indexed to the tile number, and two and
 Line 288 
 scalars are common to every part of the
  arrays to individual tiles, and the arrays indexed by tile and
  neighbor to relationships between tiles and their neighbors. \\
- \subsubsection{Scalars}
+ Scalars:
  The number of tiles in a particular topology is set with the parameter
  \code{NTILES}, and the maximum number of neighbors of any tiles by
 Line 302 
 and \varlink{exch2\_domain\_nyt}{exch2_d
  of tiles in the $x$ and $y$ global indices.  For example, the default
  setup of six tiles (Fig. \ref{fig:6tile}) has
  \code{exch2\_domain\_nxt=6} and \code{exch2\_domain\_nyt=1}.  A
- topology of twenty-four square tiles, four per subdomain (as in figure
+ topology of forty-eight tiles, eight per subdomain (as in figure
- \ref{fig:24tile}), will have \code{exch2\_domain\_nxt=12} and
+ \ref{fig:48tile}), will have \code{exch2\_domain\_nxt=12} and
- \code{exch2\_domain\_nyt=2}.  Note that these parameters express the
+ \code{exch2\_domain\_nyt=4}.  Note that these parameters express the
  tile layout in order to allow global data files that are tile-layout-neutral.
  They have no bearing on the internal storage of the arrays.  The tiles
  are stored internally in a range from \code{\varlink{bi}{bi}=(1:NTILES)} in the
  $x$ axis, and the $y$ axis variable \varlink{bj}{bj} is assumed to
  equal \code{1} throughout the package. \\
- \subsubsection{Arrays indexed to tile number}
+ Arrays indexed to tile number:
  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
 Line 343 
 files. \\
  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
+ standard cube topology and indicated by \textbf{\textsf{f}}$n$ in
- figures \ref{fig:12tile} and \ref{fig:24tile}. The
+ figures \ref{fig:6tile} and
- \varlink{exch2\_nNeighbours}{exch2_nNeighbours} variable contains a
+ \ref{fig:48tile}. \varlink{exch2\_nNeighbours}{exch2_nNeighbours}
- count of the neighboring tiles each tile has, and sets the bounds for
+ contains a count of the neighboring tiles each tile has, and sets
- looping over neighboring tiles.  And
+ 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.  \\
 Line 364 
 exchange and numerical handling for the
  corners of the cube. \\
- \subsubsection{Arrays Indexed to Tile Number and Neighbor}
+ Arrays Indexed to Tile Number and Neighbor:
  The following arrays have vectors of length \code{MAX\_NEIGHBOURS} and
  \code{NTILES} and describe the orientations between the the tiles. \\
 Line 467 
 Finally, \varlink{exch2\_itlo\_c}{exch2_
  \varlink{exch2\_jthi\_c}{exch2_jthi_c} hold the location and index
  bounds of the edge segment of the neighbor tile \code{N}'s subdomain
  that gets exchanged with the local tile \code{T}.  To take the example
- of tile \code{T=2} in the twelve-tile topology
+ of tile \code{T=2} in the forty-eight-tile topology
- (Fig. \ref{fig:12tile}): \\
+ (Fig. \ref{fig:48tile}): \\
  \begin{verbatim}
         exch2_itlo_c(4,2)=17
 Line 508 
 western halo region of \code{Tn}. The ra
  width of \code{T}'s northern edge, expanded by one into the halo. \\
- \subsection{Key Routines}
+ \subsubsection{Key Routines}
  Most of the subroutines particular to exch2 handle the exchanges
  themselves and are of the same format as those described in
 Line 538 
 issue with the scalar case. These subrou
  \code{EXCH2\_SEND\_RX1} and \code{EXCH2\_SEND\_RX2}, which do most of
  the work using the variables discussed above. \\
+ \subsubsection{Experiments and tutorials that use exch2}
+ \label{sec:pkg:exch2:experiments}
+ \begin{itemize}
+ \item{Held Suarez tutorial, in tutorial\_held\_suarez\_cs verification directory,
+ described in section \ref{sect:eg-hs} }
+ \end{itemize}

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