--- manual/s_software/text/sarch.tex	2004/01/28 19:33:04	1.11
+++ manual/s_software/text/sarch.tex	2004/01/29 15:39:49	1.15
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_software/text/sarch.tex,v 1.11 2004/01/28 19:33:04 afe Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_software/text/sarch.tex,v 1.15 2004/01/29 15:39:49 afe Exp $
 
 This chapter focuses on describing the {\bf WRAPPER} environment within which
 both the core numerics and the pluggable packages operate. The description
@@ -974,44 +974,20 @@
 of controlling and coordinating the start up of a large number
 (hundreds and possibly even thousands) of copies of the same 
 program, MPI is used. The calls to the MPI multi-process startup
-routines must be activated at compile time. This is done
-by setting the {\em ALLOW\_USE\_MPI} and {\em ALWAYS\_USE\_MPI}
-flags in the {\em CPP\_EEOPTIONS.h} file.\\
+routines must be activated at compile time.  Currently MPI libraries are 
+invoked by
+specifying the appropriate options file with the 
+{\tt-of} flag when running the {\em genmake2} 
+script, which generates the Makefile for compiling and linking MITgcm.
+(Previously this was done by setting the {\em ALLOW\_USE\_MPI} and 
+{\em ALWAYS\_USE\_MPI} flags in the {\em CPP\_EEOPTIONS.h} file.)  More
+detailed information about the use of {\em genmake2} for specifying 
+local compiler flags is located in section \ref{sect:genmake}.\\  
 
-\fbox{ 
-\begin{minipage}{4.75in}
-File: {\em eesupp/inc/CPP\_EEOPTIONS.h}\\
-CPP:  {\em ALLOW\_USE\_MPI}\\
-CPP:  {\em ALWAYS\_USE\_MPI}\\
-Parameter:  {\em nPx}\\
-Parameter:  {\em nPy}
-\end{minipage}
-} \\
-
-Additionally, compile time options are required to link in the 
-MPI libraries and header files. Examples of these options 
-can be found in the {\em genmake2} script that creates makefiles
-for compilation. When this script is executed with the {bf -mpi}
-flag it will generate a makefile that includes
-paths for search for MPI head files and for linking in 
-MPI libraries. For example the {\bf -mpi} flag on a
- Silicon Graphics IRIX system causes a
-Makefile with the compilation command
-Graphics IRIX system \begin{verbatim}
-mpif77 -I/usr/local/mpi/include -DALLOW_USE_MPI -DALWAYS_USE_MPI
-\end{verbatim}
-to be generated.
-This is the correct set of options for using the MPICH open-source
-version of MPI, when it has been installed under the subdirectory
-/usr/local/mpi.
-However, on many systems there may be several
-versions of MPI installed. For example many systems have both
-the open source MPICH set of libraries and a vendor specific native form
-of the MPI libraries. The correct setup to use will depend on the
-local configuration of your system.\\
 
 \fbox{ 
 \begin{minipage}{4.75in}
+Directory: {\em tools/build\_options}\\
 File: {\em tools/genmake2}
 \end{minipage}
 } \\
@@ -1030,7 +1006,7 @@
 in the file {\em SIZE.h}. The parameter {\em mf} specifies that a text file
 called ``mf'' will be read to get a list of processor names on
 which the sixty-four processes will execute. The syntax of this file
-is specified by the MPI distribution
+is specified by the MPI distribution.
 \\ 
 
 \fbox{ 
@@ -1081,15 +1057,20 @@
 Allocation of processes to tiles in controlled by the routine
 {\em INI\_PROCS()}. For each process this routine sets
 the variables {\em myXGlobalLo} and {\em myYGlobalLo}.
-These variables specify (in index space) the coordinate
-of the southern most and western most corner of the 
-southern most and western most tile owned by this process.
+These variables specify in index space the coordinates
+of the southernmost and westernmost corner of the 
+southernmost and westernmost tile owned by this process.
 The variables {\em pidW}, {\em pidE}, {\em pidS} and {\em pidN}
 are also set in this routine. These are used to identify
 processes holding tiles to the west, east, south and north 
 of this process. These values are stored in global storage
 in the header file {\em EESUPPORT.h} for use by
-communication routines.
+communication routines.  The above does not hold when the 
+exch2 package is used -- exch2 sets its own parameters to 
+specify the global indices of tiles and their relationships
+to each other.  See the documentation on the exch2 package
+(\ref{sec:exch2})  for
+details.
 \\
 
 \fbox{ 
@@ -1115,10 +1096,13 @@
 describes the information that is held and used.
 
 \begin{enumerate}
-\item {\bf Tile-tile connectivity information} For each tile the WRAPPER
-sets a flag that sets the tile number to the north, south, east and
+\item {\bf Tile-tile connectivity information} 
+For each tile the WRAPPER
+sets a flag that sets the tile number to the north, 
+south, east and
 west of that tile. This number is unique over all tiles in a 
-configuration. The number is held in the variables {\em tileNo}
+configuration. Except when using the cubed sphere and the exch2 package,
+the number is held in the variables {\em tileNo}
 ( this holds the tiles own number), {\em tileNoN}, {\em tileNoS},
 {\em tileNoE} and {\em tileNoW}. A parameter is also stored with each tile
 that specifies the type of communication that is used between tiles.
@@ -1141,7 +1125,13 @@
 (see figure \ref{fig:communication_primitives}). The routine 
 {\em ini\_communication\_patterns()} is responsible for setting the
 communication mode values for each tile.
-\\
+
+When using the cubed sphere configuration with the exch2 package, the 
+relationships between tiles and their communication methods are set 
+by the package in other variables.  See the exch2 package documentation 
+(\ref{sec:exch2} for details.
+
+
 
 \fbox{ 
 \begin{minipage}{4.75in}