--- manual/s_software/text/sarch.tex	2002/02/28 19:32:20	1.7
+++ manual/s_software/text/sarch.tex	2004/01/28 19:59:03	1.12
@@ -1,11 +1,11 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_software/text/sarch.tex,v 1.7 2002/02/28 19:32:20 cnh Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_software/text/sarch.tex,v 1.12 2004/01/28 19:59:03 afe Exp $
 
 This chapter focuses on describing the {\bf WRAPPER} environment within which
 both the core numerics and the pluggable packages operate. The description
 presented here is intended to be a detailed exposition and contains significant
 background material, as well as advanced details on working with the WRAPPER. 
-The tutorial sections of this manual (see Chapters
-\ref{chap:tutorialI}, \ref{chap:tutorialII} and \ref{chap:tutorialIII}) 
+The tutorial sections of this manual (see sections
+\ref{sect:tutorials}  and \ref{sect:tutorialIII}) 
 contain more succinct, step-by-step instructions on running basic numerical
 experiments, of varous types, both sequentially and in parallel. For many 
 projects simply starting from an example code and adapting it to suit a 
@@ -97,7 +97,7 @@
 \resizebox{!}{4.5in}{\includegraphics{part4/fit_in_wrapper.eps}}
 \end{center}
 \caption{
-Numerical code is written too fit within a software support
+Numerical code is written to fit within a software support
 infrastructure called WRAPPER. The WRAPPER is portable and
 can be specialized for a wide range of specific target hardware and 
 programming environments, without impacting numerical code that fits
@@ -120,7 +120,7 @@
 (UMA) and non-uniform memory access (NUMA) designs. Significant work has also 
 been undertaken on x86 cluster systems, Alpha processor based clustered SMP 
 systems, and on cache-coherent NUMA (CC-NUMA) systems from Silicon Graphics. 
-The MITgcm code, operating within the WRAPPER, is also used routinely used on 
+The MITgcm code, operating within the WRAPPER, is also routinely used on 
 large scale MPP systems (for example T3E systems and IBM SP systems). In all 
 cases numerical code, operating within the WRAPPER, performs and scales very 
 competitively with equivalent numerical code that has been modified to contain 
@@ -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
@@ -781,7 +787,7 @@
 forty grid points in y. The two sub-domains in each process will be computed 
 sequentially if they are given to a single thread within a single process.
 Alternatively if the code is invoked with multiple threads per process
-the two domains in y may be computed on concurrently.
+the two domains in y may be computed concurrently.
 \item
 \begin{verbatim}
       PARAMETER (
@@ -817,6 +823,7 @@
 WRAPPER is shown in figure \ref{fig:wrapper_startup}.
 
 \begin{figure}
+{\footnotesize
 \begin{verbatim}
 
        MAIN  
@@ -845,6 +852,7 @@
 
 
 \end{verbatim}
+}
 \caption{Main stages of the WRAPPER startup procedure.
 This process proceeds transfer of control to application code, which
 occurs through the procedure {\em THE\_MODEL\_MAIN()}.
@@ -927,7 +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}\\
@@ -966,45 +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 
@@ -1424,6 +1407,7 @@
 
 WRAPPER layer.
 
+{\footnotesize
 \begin{verbatim}
 
        MAIN  
@@ -1451,9 +1435,11 @@
        |--THE_MODEL_MAIN   :: Numerical code top-level driver routine
 
 \end{verbatim}
+}
 
 Core equations plus packages.
 
+{\footnotesize
 \begin{verbatim}
 C
 C
@@ -1792,6 +1778,7 @@
 C                     :: events.
 C 
 \end{verbatim}
+}
 
 \subsection{Measuring and Characterizing Performance}