--- manual/s_phys_pkgs/text/exch2.tex 2004/10/12 18:16:03 1.22 +++ manual/s_phys_pkgs/text/exch2.tex 2005/07/18 20:45:27 1.24 @@ -1,4 +1,4 @@ -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.22 2004/10/12 18:16:03 edhill Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/text/exch2.tex,v 1.24 2005/07/18 20:45:27 molod Exp $ % $Name: $ %% * Introduction @@ -10,15 +10,11 @@ %% 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} - -\end{rawhtml} -\subsection{Introduction} +\subsubsection{Introduction} The \texttt{exch2} package extends the original cubed sphere topology configuration to allow more flexible domain decomposition and @@ -45,57 +41,46 @@ \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: +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$32 cube sides -- please contact - \begin{rawhtml} - - \end{rawhtml} -\begin{verbatim} -MITgcm-support@mitgcm.org -\end{verbatim} - \begin{rawhtml} \end{rawhtml} - if you want to generate files for other configurations. - -\item As always when compiling MITgcm, the file \file{SIZE.h} must be - placed where \file{genmake2} will find it. In particular for exch2, - the domain decomposition specified in \file{SIZE.h} must correspond - with the particular configuration's topology specified in + symbolically linked by the \file{genmake2} script. The safest place to + put these is the directory indicated in the \code{-mods=DIR} command + line modifier (typically \file{../code}), or the build directory. + The default versions of these files reside in \file{pkg/exch2} and + are linked automatically if no other versions exist elsewhere in the + build path, but they should be left untouched to avoid breaking + configurations other than the one you intend to modify.\\ + +$\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: @@ -111,7 +96,7 @@ -\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 @@ -197,7 +182,7 @@ -\subsection{exch2, SIZE.h, and Multiprocessing} +\subsubsection{exch2, SIZE.h, and Multiprocessing} \label{sec:exch2mpi} Once the topology configuration files are created, the Fortran @@ -230,12 +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 @@ -278,7 +271,7 @@ -\subsection{Key Variables} +\subsubsection{Key Variables} The descriptions of the variables are divided up into scalars, one-dimensional arrays indexed to the tile number, and two and @@ -288,7 +281,7 @@ 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 @@ -311,11 +304,11 @@ $x$ 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 @@ -343,11 +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. \\ @@ -364,7 +357,7 @@ 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. \\ @@ -508,7 +501,7 @@ 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