/[MITgcm]/manual/s_software/text/sarch.tex

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-revision 1.10 by edhill,
Thu Aug  7 18:27:52 2003 UTC
+revision 1.14 by afe,
Wed Jan 28 20:38:28 2004 UTC
 Line 661 
 Within a {\em bi}, {\em bj} loop
  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
+,{\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
-Line 929 
 File: {\em eesupp/inc/MAIN\_PDIRECTIVES1
+Line 935 
 File: {\em eesupp/inc/MAIN\_PDIRECTIVES1
  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}\\
-Line 968 
 critical communication. However, in orde
+Line 974 
 critical communication. However, in orde
  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
+ routines must be activated at compile time.  Currently MPI libraries are
- by setting the {\em ALLOW\_USE\_MPI} and {\em ALWAYS\_USE\_MPI}
+ invoked by
- flags in the {\em CPP\_EEOPTIONS.h} file.\\
+ specifying the appropriate options file with the
+ \begin{verbatim}-of\end{verbatim} flag when running the {\em genmake2}
- \fbox{
+ script, which generates the Makefile for compiling and linking MITgcm.
- \begin{minipage}{4.75in}
+ (Previously this was done by setting the {\em ALLOW\_USE\_MPI} and
- File: {\em eesupp/inc/CPP\_EEOPTIONS.h}\\
+ {\em ALWAYS\_USE\_MPI} flags in the {\em CPP\_EEOPTIONS.h} file.)  More
- CPP:  {\em ALLOW\_USE\_MPI}\\
+ detailed information about the use of {\em genmake2} for specifying
- CPP:  {\em ALWAYS\_USE\_MPI}\\
+ local compiler flags is located in section 3 ??\\
- 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
-Line 1083 
 are also set in this routine. These are
+Line 1064 
 are also set in this routine. These are
  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 exch2 docs for details??.
  \\
  \fbox{
-Line 1112 
 describes the information that is held a
+Line 1096 
 describes the information that is held a
  \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 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.
-Line 1137 
 of the WRAPPER exchange primitive
+Line 1122 
 of the WRAPPER exchange primitive
  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 docs for details.??
  \fbox{
  \begin{minipage}{4.75in}
  File: {\em eesupp/src/ini\_communication\_patterns.F}\\

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