/[MITgcm]/MITgcm/doc/devel_HOWTO.sgml

Diff of /MITgcm/doc/devel_HOWTO.sgml

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-revision 1.7 by edhill,
Tue Apr  6 04:12:00 2004 UTC
+revision 1.10 by jmc,
Thu Jan 21 23:59:17 2010 UTC
 Line 22
            Initial version.
          </revremark>
        </revision>
+       <revision>
+         <revnumber>0.02</revnumber>
+         <date>2010-01-21</date>
+         <authorinitials>jmc</authorinitials>
+         <revremark>
+           update links.
+         </revremark>
+       </revision>
      </revhistory>
      <abstract>
-Line 37
+Line 45
      <sect2>
        <title>New Versions of This Document</title> <para>You can
        obtain the latest version of this document <ulink
-       url="http://mitgcm.org/dev_docs/devel_HOWTO/">online</ulink> in
+       url="http://mitgcm.org/public/docs.html">online</ulink> in
        various formats.</para>
      </sect2>
      <sect2>
-Line 56
+Line 64
        <title>User Manual</title>
        <para>Before jumping into development, please familiarize yourself with
-         the <ulink url="http://mitgcm.org/docs.html"> MITgcm user manual
+         the <ulink url="http://mitgcm.org/public/docs.html"> MITgcm user manual
          </ulink>.  This document contains volumes of useful information and is
          included here by reference.</para>
-Line 130
+Line 138
     e|- tools
     ?|  tutorial_examples        documented tests
      |                             only populated on release1 branch
-     |                             and not validated during "testscript"
+     |                             and not validated during "testreport"
      '- utils
         verification             std tests
-Line 182
+Line 190
        <title>Branches</title>
        <para>As shown in the online <ulink
-       url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/doc/tag-index?graph=1.174">
+       url="http://mitgcm.org/viewvc/MITgcm/MITgcm/doc/tag-index?view=graph">
        ViewCVS-generated tree</ulink>, the MITgcm codebase is split into to two
        branches or "lines" under which development proceeds.  These two lines are
        referred to as the "MAIN" and "ecco" versions of the code.  While not
-Line 216
+Line 224
          <listitem>
            <para>The developer then runs the <ulink
-           url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/verification/testscript">
+           url="http://mitgcm.org/viewvc/MITgcm/MITgcm/verification/testreport">
-           testscript</ulink> shell script to see if any problems are introduced.
+           testreport</ulink> shell script to see if any problems are introduced.
            While not intended to be exhaustive, the test cases within the
            verification directory do provide some indication whether gross errors
            have been introduced.
-Line 232
+Line 240
              <listitem>
                <para>adds a "checkpointXY_pre" comment (where X is a checkpoint
                number and Y is a letter) to the <ulink
-               url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/doc/tag-index">
+               url="http://mitgcm.org/viewvc/MITgcm/MITgcm/doc/tag-index">
                tag-index</ulink> file and checks it into the CVS
                repository</para>
              </listitem>
-Line 290 
 checkpoint50d_pre
+Line 298 
 checkpoint50d_pre
    $ export CVS_RSH=ssh
    $ export CVSROOT=':ext:NAME@mitgcm.org:/u/gcmpack'
    $ mkdir scratch
-   $ cvs co MITgcm manual mitgcm.org
+   $ cvs co -P MITgcm manual mitgcm.org
  </screen>
        <para>These commands extract the necessary information from the CVS server
-Line 787 
 checkpoint50d_pre
+Line 795 
 checkpoint50d_pre
                special command option (see "-command" below) to invoke the MPI
                executable.  Examples of PBS scripts using MPI with testreport can be
                found in the <ulink
-               url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
+               url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
                MITgcm-contrib area</ulink></para>
              </listitem>
            </varlistentry>
-Line 799 
 checkpoint50d_pre
+Line 807 
 checkpoint50d_pre
                output.txt" is not sufficient.  This option allows a more general
                command (or shell script) to be invoked.  Examples of PBS scripts
                using MPI with testreport can be found in the <ulink
-               url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
+               url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
                MITgcm-contrib area</ulink></para>
              </listitem>
            </varlistentry>
-Line 886 
 o  Each package gets its runtime configu
+Line 894 
 o  Each package gets its runtime configu
     Package runtime config. options are imported
     into a common block held in a header file
     called "${PKG}.h".
+    Note: In some packages, the header file "${PKG}.h" is splitted
+    into "${PKG}_PARAMS.h" that contains the package parameters and
+    ${PKG}_VARS.h" for the field arrays.
  o  The core driver part of the model can check
     for runtime enabling or disabling of individual packages
-Line 908 
 CPP Flags
+Line 919 
 CPP Flags
 . Within the core driver code flags of the form
         ALLOW_${PKG} are used to include or exclude
         whole packages. The ALLOW_${PKG} flags are included
-        from a PKG_CPP_OPTIONS block which is currently
+        from a PACKAGES_CONFIG.h file that is automatically
+        generated by genmake2 (see genmake2 section).
         held in-line in the CPP_OPTIONS.h header file.
         e.g.
         Core model code .....
+        #include "PACKAGES_CONFIG.h"
         #include "CPP_OPTIONS.h"
           :
           :
-Line 925 
 CPP Flags
+Line 938 
 CPP Flags
 . Within an individual package a header file,
         "${PKG}_OPTIONS.h", is used to set CPP flags
-        specific to that package. It is not recommended
+        specific to that package. It also includes
-        to include this file in "CPP_OPTIONS.h".
+        "PACKAGES_CONFIG.h" and "CPP_OPTIONS.h".
  Package Boot Sequence
-Line 978 
 Package Output
+Line 991 
 Package Output
          #ifdef ALLOW_${PKG}
            if ( use${Pkg} )
-      &       CALL ${PKG}_DIAGS( )
+      &       CALL ${PKG}_OUTPUT( )
          #endif
 . S/R PACKAGES_WRITE_PICKUP()
-Line 994 
 Description
+Line 1007 
 Description
        - ${PKG}_READPARMS()
      is responsible for reading
      in the package parameters file data.${pkg}, and storing
-     the package parameters in "${PKG}.h".
+     the package parameters in "${PKG}.h" (or in "${PKG}_PARAMS.h").
      -> called from INITIALISE_FIXED in PACKAGES_READPARMS
       - ${PKG}_INIT_FIXED()
-Line 1024 
 Description
+Line 1037 
 Description
       use for e.g. ${PKG}_INI_VARS, ${PKG}_INIT_VARIABLES, or the old
       form ${PKG}_INIT
-      - ${PKG}_DIAGS()
+      - ${PKG}_OUTPUT( )
-      is responsible for writing time-average diagnostics to output
+      is responsible for writing time-average fields to output files
-      files (but the cumulating step is done within the package main S/R).
+      (but the cumulating step is done within the package main S/R).
       Can also contain other diagnostics (.e.g. CALL ${PKG}_MONITOR)
       and write snap-shot fields that are hold in common blocks. Other
       temporary fields are directly dump to file where they are available.
-      NOTE: this part does not yet have a standard form and should be called
+      NOTE: 1) the S/R old name ${PKG}_DIAGS is used in some packages
-        from a package dedicated S/R such as PACKAGE_WRITE_DIAGS
+               but is beeing replaced by ${PKG}_OUTPUT
+               to avoid confusion with pkg/diagnostics functionality.
+) the output part is not yet in a standard form and might still
+               evolve a lot.
      -> called within DO_THE_MODEL_IO
       - ${PKG}_WRITE_PICKUP()
-Line 1058 
 Summary
+Line 1074 
 Summary
    -----------------------
    * ${PKG}_OPTIONS.h     has further package-specific CPP options
    * ${PKG}.h             package-specific common block variables, fields
+    or  ${PKG}_PARAMS.h   package-specific common block parameters
+    and ${PKG}_VARS.h     package-specific common block fields
  - FORTRAN source files
    -----------------------
-Line 1066 
 Summary
+Line 1084 
 Summary
    * ${pkg}_check.F        checks package dependencies and consistencies
    * ${pkg}_init_varia.F   initialises package-related fields
    * ${pkg}_... .F         package source code
-   * ${pkg}_diags.F        write diagnostics to file.
+   * ${pkg}_output.F       write output to file.
    * ${pkg}_write_pickup.F write a package pickup file to restart the model
+   New: Subroutine in one package (pkgA) that only contains code which
+        is connected to a 2nd package (pkgB) (e.g.: gmredi_diagnostics_init.F)
+        will be named: pkgA_pkgB_something.F
  - parameter file
    -----------------------
    * data.${pkg}          parameter file

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