--- manual/s_software/text/sarch.tex	2003/08/07 18:27:52	1.10
+++ manual/s_software/text/sarch.tex	2004/01/28 20:27:54	1.13
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_software/text/sarch.tex,v 1.10 2003/08/07 18:27:52 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_software/text/sarch.tex,v 1.13 2004/01/28 20:27:54 afe Exp $
 
 This chapter focuses on describing the {\bf WRAPPER} environment within which
 both the core numerics and the pluggable packages operate. The description
@@ -661,6 +661,12 @@
 computation is performed concurrently over as many processes and threads
 as there are physical processors available to compute.
 
+An exception to the the use of {\em bi} and {\em bj} in loops arises in the
+exchange routines used when the exch2 package is used with the cubed 
+sphere.  In this case {\em bj} is generally set to 1 and the loop runs from 
+1,{\em bi}.  Within the loop {\em bi} is used to retrieve the tile number,
+which is then used to reference exchange parameters.
+
 The amount of computation that can be embedded
 a single loop over {\em bi} and {\em bj} varies for different parts of the
 MITgcm algorithm. Figure \ref{fig:bibj_extract} shows a code extract
@@ -929,7 +935,7 @@
 File: {\em eesupp/inc/MAIN\_PDIRECTIVES2.h}\\
 File: {\em model/src/THE\_MODEL\_MAIN.F}\\
 File: {\em eesupp/src/MAIN.F}\\
-File: {\em tools/genmake}\\
+File: {\em tools/genmake2}\\
 File: {\em eedata}\\
 CPP:  {\em TARGET\_SUN}\\
 CPP:  {\em TARGET\_DEC}\\
@@ -968,45 +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 
+\begin{verbatim}-of\end{verbatim} 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 3 ??\\  
 
-\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 genmake} 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}
-File: {\em tools/genmake}
+File: {\em tools/genmake2}
 \end{minipage}
 } \\
 \paragraph{\bf Execution} The mechanics of starting a program in 
@@ -1083,7 +1064,10 @@
 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.
 \\
 
 \fbox{