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-revision 1.7 by edhill,
Tue Apr  6 04:12:00 2004 UTC
+revision 1.14 by jmc,
Fri May 28 01:47:32 2010 UTC
 Line 1
  <!DOCTYPE ARTICLE PUBLIC "-//OASIS//DTD DocBook V4.1//EN">
+ <!--
+  $Header$
+  $Name$
+ -->
  <article id="MITgcm-Development-HOWTO">
-Line 22
+Line 26
            Initial version.
          </revremark>
        </revision>
+       <revision>
+         <revnumber>0.02</revnumber>
+         <date>2010-01-21</date>
+         <authorinitials>jmc</authorinitials>
+         <revremark>
+           update links.
+         </revremark>
+       </revision>
+       <revision>
+         <revnumber>0.03</revnumber>
+         <date>2010-04-25</date>
+         <authorinitials>jmc</authorinitials>
+         <revremark>
+           Add subsection "Developer settings" (under CVS Repository).
+         </revremark>
+       </revision>
      </revhistory>
      <abstract>
-Line 37
+Line 57
      <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 76
        <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 94
+Line 114
    <sect1 id="cvs">
      <title>CVS Repository</title>
      <sect2>
        <title>Layout</title>
-Line 104
+Line 125
        others.  The tree currently resembles:</para>
  <programlisting>gcmpack/
-   MITgcm-contrib        contributed code
+   CVSROOT               -hidden-
-   CS-regrid             goes into utils
-   cvspolicy.html        -save-
-   CVSROOT               -save-
-   development           experimental stuff
-   manual                -save-
-   misc                  -?-
    MITgcm                code
-        adjoint                  fold into genmake
+        bin                      empty
-        bin                      stub for ecco build
+        doc                      basic developpment documentation
-        compare01                old from 20th century
+        eesupp                   execution environment support code (wrapper)
-        diags                    timeave f77 in pkgs now
+        exe                      empty
-        doc                      tags -- connect to real docs?
+        jobs                     runtime shell scripts for
-        eesupp                   cnh?
+                                   various platforms (not maintained)
-        exe                      ecco user build
+        lsopt                    line search
-     ,- jobs                     runtime shell scripts for
+        model                    main dynamics (core)
-     |                             various platforms
+        optim                    line search interface
-     |  lsopt                    line search
+        pkg                      alternate and optional numerics, etc.
-    m|  model                    main dynamics (core)
+        tools                    scripts to build (and test)
-    e|    optimization_drivers   ?
+        utils                    pre/post processing tools (matlab, ..)
-    r|  optim                    line search interface
+        verification             standard regression tests + examples
-    g|  pkg                      alternate and optional numerics, etc.
+                                       + documented examples (tutorials)
-    e|- tools
+        tutorial_examples        (only in release1 branch)
-    ?|  tutorial_examples        documented tests
-     |                             only populated on release1 branch
-     |                             and not validated during "testscript"
-     '- utils
-        verification             std tests
+   MITgcm_contrib        contributed code
-   mitgcmdoc -> manual   -remove-
+   acesgrid.org          build acesgrid web site
+   development           experimental stuff
+   gfd_lab               -?-
+   manual                source of MITgcm documentation
    mitgcm.org            build web site
-   models                -?-
+   old_develop           old and early development source
-   packages              -?-
+        misc                 -?-
-   preprocess            -?-
+        models               -?-
-   tmp                   -?-
+        packages             -?-
+        preprocess           -?-
+   pdfs                  some pdfs
+   planetinabottle.org   unfinished web site
+   www.ecco-group.org    build ecco web site ?
  </programlisting>
+  <!--
        <para>Efforts are underway to reduce the complexity.</para>
+ -->
      </sect2>
-Line 182
+Line 202
        <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/model/src/forward_step.F?view=graph">
-       ViewCVS-generated tree</ulink>, the MITgcm codebase is split into to two
+       ViewCVS-generated tree</ulink>, the MITgcm codebase is split into
-       branches or "lines" under which development proceeds.  These two lines are
+       branches or "lines" under which development proceeds.  The main line
-       referred to as the "MAIN" and "ecco" versions of the code.  While not
+       of development is referred to as the "MAIN" version of the code.
-       identical, the bulk of the MAIN and ecco lines are composed of files from
-       the same codebase.
        </para>
        <para>Periodically, a "Release" branch is formed from the "MAIN"
        development branch.  This is done in order to create a relatively stable
        reference point for both users and developers.  The intent is that once a
-       relese branch has been created, only bug-fixes will be added to it.
+       release branch has been created, only bug-fixes will be added to it.
        Meanwhile, development (which might "break" or otherwise render invalid
        the documentation, tutorials, and/or examples contained within a release
-       branch) is allowed to continue along the MAIN and ecco lines.</para>
+       branch) is allowed to continue along the MAIN line.</para>
+     </sect2>
+     <sect2>
+       <title> Developer settings </title>
+       <para>CVS is a convenient tool to keep up-to-date a personal copy of the
+       MITgcm code (see: <ulink url="http://mitgcm.org/public/using_cvs.html">
+       using CVS </ulink>). The same tool is used by developers to
+       incorporate any change into the repository. However, this later
+       function requires specific settings, as detailed here after:</para>
+       <orderedlist>
+         <listitem>
+           <para> You will need an account (loggin access) to the server
+            "mitgcm.org" with the proper group setting (e.g.,
+             group "gcmctrb" to add/modify code into MITgcm_contrib).
+             This kind of account is granted only upon well motivated request.
+             The access to the server mitgcm.org is through ssh-key authorization
+             which will need to be set properly on both side (on your local machine
+             and on your server account). You need to be able to
+             to ssh to mitgcm.org (or <filename>ssh MY_USER_NAME@mitgcm.org</filename>
+             in case of different user-name on both sides) to proceed further.</para>
+         </listitem>
+         <listitem>
+           <para> You need to register to the
+         <ulink url="http://mitgcm.org/mailman/listinfo/mitgcm-cvs">
+       mitgcm-cvs </ulink> mailing list.
+           This ensures that other developers will receive email notification
+            when you make changes; you will also receive as well such email
+            when others make changes to the repository.
+           </para>
+         </listitem>
+         <listitem>
+           <para> It is highly recommended that you register also to the
+         <ulink url="http://mitgcm.org/mailman/listinfo/mitgcm-devel">
+       mitgcm-devel </ulink> mailing list (expect a short delay for
+        this request to be processed).
+           This list is intended for developer discussions.
+           </para>
+         </listitem>
+         <listitem>
+           <para> The standard anonymous mode (using "cvsanon", as mentionned
+         <ulink url="http://mitgcm.org/public/source_code.html">
+       here </ulink>) does not allow check-in ("cvs commit") permission.
+          Instead, you will need to set our CVS environment as follow:</para>
+ <screen>
+   $ export CVS_RSH=ssh
+   $ export CVSROOT=':ext:MY_USER_NAME@mitgcm.org:/u/gcmpack'
+ </screen>
+           <para> After downloading a directory, e.g.: <filename>myCopy</filename>,
+            from the CVS repository (e.g.,
+             <filename>MITgcm_contrib/thisPart</filename>) using the command:</para>
+ <screen>
+   $ cvs co -P -d myCopy MITgcm_contrib/thisPart
+ </screen>
+           <para> the type of CVS environment which has been used
+            is stored in the file <filename>myCopy/CVS/Root</filename>
+            and makes it difficult to re-use, for cvs-commit purpose,
+            a cvs local copy (<filename>myCopy</filename>) which was obtained
+            using the CVS anonymous mode.</para>
+         </listitem>
+         <listitem>
+           <para> At this stage, you should be able to send your modified source
+           file (e.g., <filename>src_file</filename>) from your local copy directory
+           (<filename>myCopy</filename>) to the CVS repository
+           (<filename>MITgcm_contrib/thisPart</filename>) using the command
+           "cvs commit":</para>
+ <screen>
+   $ cd myCopy
+   $ cvs -n update        (optional; check if new changes have been made)
+   $ cvs diff src_file    (optional; list your changes)
+   $ cvs commit src_file
+ </screen>
+           <para> It is essential that you provide a short description of the
+           changes you made to <filename>src_file</filename> as you check-in
+           this file (the "cvs commit" command automatically opens your standard
+           editor for this purpose).</para>
+         </listitem>
+       </orderedlist>
      </sect2>
      <sect2>
-       <title>Tagging</title>
+       <title>Main code development</title>
+       <para><emphasis>(formerly named "Tagging" ; this section needs an update)
+         </emphasis></para>
        <para>The intent of tagging is to create "known-good" checkpoints that
        developers can use as references.  Traditionally, MITgcm tagging has
-Line 216
+Line 320
          <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 336
              <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 277 
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+Line 381 
 checkpoint50d_pre
    </sect1>
-   <sect1 id="documentation">
-     <title>Editing the Documentation</title>
-     <sect2 id="documentation_getting">
-       <title>Getting the Docs and Code</title>
-       <para>The first step towards editing the documentation is to checkout a
-       copy of code, docs, and build scripts from the CVS server using:</para>
- <screen>
-   $ export CVS_RSH=ssh
-   $ export CVSROOT=':ext:NAME@mitgcm.org:/u/gcmpack'
-   $ mkdir scratch
-   $ cvs co MITgcm manual mitgcm.org
- </screen>
-       <para>These commands extract the necessary information from the CVS server
-       and create a temporary (called <filename>scratch</filename>) directory for
-       the storage of the HTML and other files that will be created.  Please note
-       that you must either create <filename>scratch</filename> as shown or edit
-       the various <filename>Makefile</filename>s and scripts used to create the
-       documentation.</para>
-     </sect2>
-     <sect2>
-       <title>Editing the Documentation</title>
-       <para>The documentation is contained in the <filename>manual</filename>
-       directory in a raw LaTeX format.  The main document is
-       <filename>manual.tex</filename> and it uses <command>\input{}</command>s
-       to include the chapters and subsections.</para>
-       <para>Since the same LaTeX source is used to produce PostScript, PDF, and
-       HTML output, care should be taken to follow certain conventions.  Two of
-       the most important are the usage of the <command>\filelink{}{}</command>
-       and <command>\varlink{}{}</command> commands.  Both of these commands have
-       been defined to simplify the connection between the automatically
-       generated ("code browser") HTML and the HTML version of the manual
-       produced by LaTeX2HTML.  They each take two arguments (corresponding to
-       the contents of the two sets of curly braces) which are the text that the
-       author wishes to be "wrapped" within the link, and a specially formatted
-       link thats relative to the <filename>MITgcm</filename> directory within
-       the CVS tree.</para>
-       <para>The result is a command that resembles either</para>
-       <orderedlist>
-         <listitem>
-           <para>a reference to a variable or subroutine name such as
-           <command>\varlink{tRef}{tRef}</command>, or </para>
-         </listitem>
-         <listitem>
-           <para>a reference to a file such as
-               <command>\varlink{tRef}{path-to-the-file_name.F}</command>
-               where the absolute path to the file is of the form
-               <filename>/foo/MITgcm/path/to/the/file_name.F</filename></para>
-               <para>(please note how the leading "/foo/MITgcm"
-               component of the path is dropped leaving the path
-               <emphasis>relative</emphasis> to the head of the code
-               directory and each directory separator "/" is turned
-               into a "-")</para>
-         </listitem>
-       </orderedlist>
-     </sect2>
-     <sect2>
-       <title>Building the Documentation</title>
-       <para>Given the directory structure of <xref
-       linkend="documentation_getting">, the entire documentation for the web
-       site can be built using:</para>
- <screen>
-   $ cd mitgcm.org/devel/buildweb
-   $ make All
- </screen>
-       <para>Which builds the PDF from the LaTeX source, creates the HTML output
-       from the LaTeX source, parses the FORTRAN code base to produce a
-       hyperlinked HTML version of the source, and then determines the
-       cross-linking between the various HTML components.</para>
-       <para>If there are no errors, the result of the build process (which can
-       take 30+ minutes on a P4/2.5Ghz) will be contained within a single
-       directory called <filename>scratch/dev_docs</filename>.  This is a freshly
-       built version of the entire on-line users manual.  If you have the correct
-       permissions, it can be directly copied to the web server area:</para>
- <screen>
-   $ mv scratch/dev_docs /u/u0/httpd/html
- </screen>
-       <para>and the update is complete.</para>
-     </sect2>
-   </sect1>
    <sect1 id="coding">
      <title>Coding for MITgcm</title>
-Line 392 
 checkpoint50d_pre
+Line 394 
 checkpoint50d_pre
          For MITgcm, the process is similar.  Typical commands are:</para>
  <screen>
-   $ genmake -mods=../code
+   $ genmake2 -mods=../code
    $ make depend
    $ make
  </screen>
-Line 403 
 checkpoint50d_pre
+Line 405 
 checkpoint50d_pre
        <sect3 id="genmake">
          <title>The <filename>genmake2</> Utility</title>
-         <para><emphasis>Please note that the older <filename>genmake</> is
+         <para><emphasis>(Note: the older <filename>genmake</>
-             deprecated and will eventually be replaced by <filename>genmake2</>.
+             has been replaced by <filename>genmake2</>)</emphasis></para>
-             This HOWTO only describes the newer tool.</emphasis></para>
          <para>The first step in any MITgcm build is to create a Unix-style
            <filename>Makefile</filename> which will be parsed by
-Line 461 
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+Line 462 
 checkpoint50d_pre
              <para>an "options file" as specified by the command-line option
                <filename>-optfile='FILENAME'</filename></para>
            </listitem>
+           <listitem>
+             <para> a <filename>packages.conf</filename> file (in the current
+               directory or in one of the "MODS" directories, see below)
+               which contains the specific list of packages to compile
+             </para>
+           </listitem>
          </orderedlist>
          <para>then checking certain dependency rules (the package dependencies),
-Line 514 
 checkpoint50d_pre
+Line 521 
 checkpoint50d_pre
            </varlistentry>
            <varlistentry>
-             <term><filename>-pdepend=/PATH/FILENAME</></term>
-             <listitem>
-               <para>This specifies the dependency file used for packages.  If
-               not specified, the default dependency file is
-               <filename>$ROOTDIR/pkg/pkg_depend</>.  The syntax for this file is
-               parsed on a line-by-line basis where each line containes either a
-               comment ("#") or a simple "PKGNAME1 (+|-)PKGNAME2" pairwise rule
-               where the "+" or "-" symbol specifies a "must be used with" or a
-               "must not be used with" relationship, respectively.  If no rule is
-               specified, then it is assumed that the two packages are compatible
-               and will function either with or without each other.</para>
-             </listitem>
-           </varlistentry>
-           <varlistentry>
-             <term><filename>-pdefault=PKG</></term>
-             <term><filename>-pdefault='PKG1 [PKG2 PKG3 ...]'</></term>
-             <listitem>
-               <para>This option specifies the default set of packages
-               to be used.  If not set, the default package list will
-               be read from
-               <filename>$ROOTDIR/pkg/pkg_default</>.</para>
-             </listitem>
-           </varlistentry>
-           <varlistentry>
              <term><filename>-adof=/path/to/file</></term>
              <term><filename>-adoptfile=/path/to/file</></term>
              <listitem>
-Line 568 
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+Line 548 
 checkpoint50d_pre
                  will be overridden by any identically-named sources within the
                  "MODS" directories.  The order of precedence for this
                  "name-hiding" is as follows:</para>
                <itemizedlist>
                  <listitem><para>"MODS" directories (in the order given)
                    </para></listitem>
-Line 580 
 checkpoint50d_pre
+Line 559 
 checkpoint50d_pre
                  <listitem><para>The "standard dirs" (which may have been
                      specified by the "-standarddirs" option)</para></listitem>
                </itemizedlist>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term><filename>-pgroups=/PATH/FILENAME</></term>
+             <listitem>
+               <para>This option specifies the file where package groups are
+               defined.  If not set, the package-groups definition will
+               be read from
+               <filename>$ROOTDIR/pkg/pkg_groups</>.</para>
+               <para>
+               It also contains the default list of packages (defined
+               as the group <filename>"default_pkg_list"</>) which is used
+               when no specific package list (file: <filename>packages.conf</>)
+               is found in current directory or in any "MODS" directory.
+               </para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term><filename>-pdepend=/PATH/FILENAME</></term>
+             <listitem>
+               <para>This specifies the dependency file used for packages.  If
+               not specified, the default dependency file is
+               <filename>$ROOTDIR/pkg/pkg_depend</>.  The syntax for this file is
+               parsed on a line-by-line basis where each line containes either a
+               comment ("#") or a simple "PKGNAME1 (+|-)PKGNAME2" pairwise rule
+               where the "+" or "-" symbol specifies a "must be used with" or a
+               "must not be used with" relationship, respectively.  If no rule is
+               specified, then it is assumed that the two packages are compatible
+               and will function either with or without each other.</para>
              </listitem>
            </varlistentry>
-Line 606 
 checkpoint50d_pre
+Line 616 
 checkpoint50d_pre
          <para>In general, it is best to use <filename>genmake2</> on a "clean"
            directory that is free of all source (*.[F,f],*.[F,f]90) and header
            (*.h,*.inc) files.  Generally, this can be accomplished in an
-           "un-clean" directory by running "make CLEAN" followed by "make
+           "un-clean" directory by running "make Clean" followed by "make
            makefile".</para>
        </sect3>
-Line 619 
 checkpoint50d_pre
+Line 629 
 checkpoint50d_pre
            simulator) executable using:</para>
  <screen>
-   $ make CLEAN
+   $ make Clean
    $ make depend
    $ make
  </screen>
-         <para>The "make CLEAN" step will remove any stale source files, include
+         <para>The "make Clean" step will remove any stale source files, include
            files, and links.  It is strongly recommended for "un-clean"
            directories which may contain the (perhaps partial) results of
-           previous builds.  Such "debris" can interfere with the next stage of
+           previous builds. Such "debris" can interfere with the next stage of
-           the build.</para>
+           the build.
+           A more agressive cleaning option, "make CLEAN", can be used to also
+           remove the executable and output files from a previous run.</para>
          <para>The "make depend" step will create a large number of symbolic
            links from the local directory to the source file locations.  It also
-Line 787 
 checkpoint50d_pre
+Line 799 
 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 811 
 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 826 
 checkpoint50d_pre
+Line 838 
 checkpoint50d_pre
          the generic fluid dynamical engine.</para>
        <para>The MITgcmUV packaging structure is described below using generic
-         package names ${pkg}.  A concrete examples of a package is the code for
+         package names ${pkg}. A concrete examples of a package is the code for
          implementing GM/Redi mixing. This code uses the package name</para>
      </sect2>
-Line 886 
 o  Each package gets its runtime configu
+Line 898 
 o  Each package gets its runtime configu
     Package runtime config. options are imported
     into a common block held in a header file
     called "${PKG}.h".
+    Note: In some packages, the header file "${PKG}.h" is splitted
+    into "${PKG}_PARAMS.h" that contains the package parameters and
+    ${PKG}_VARS.h" for the field arrays.
  o  The core driver part of the model can check
     for runtime enabling or disabling of individual packages
-Line 908 
 CPP Flags
+Line 923 
 CPP Flags
 . Within the core driver code flags of the form
         ALLOW_${PKG} are used to include or exclude
         whole packages. The ALLOW_${PKG} flags are included
-        from a PKG_CPP_OPTIONS block which is currently
+        from a PACKAGES_CONFIG.h file that is automatically
+        generated by genmake2 (see genmake2 section).
         held in-line in the CPP_OPTIONS.h header file.
         e.g.
         Core model code .....
+        #include "PACKAGES_CONFIG.h"
         #include "CPP_OPTIONS.h"
           :
           :
-Line 925 
 CPP Flags
+Line 942 
 CPP Flags
 . Within an individual package a header file,
         "${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 995 
 Package Output
          #ifdef ALLOW_${PKG}
            if ( use${Pkg} )
-      &       CALL ${PKG}_DIAGS( )
+      &       CALL ${PKG}_OUTPUT( )
          #endif
 . S/R PACKAGES_WRITE_PICKUP()
-Line 994 
 Description
+Line 1011 
 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 1041 
 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 1078 
 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 1088 
 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
-Line 1077 
 Summary
+Line 1103 
 Summary
    </sect1>
+   <sect1 id="documentation">
+     <title>Editing the Documentation</title>
+     <sect2 id="documentation_getting">
+       <title>Getting the Docs and Code</title>
+       <para>The first step towards editing the documentation is to checkout a
+       copy of code, docs, and build scripts from the CVS server using:</para>
+ <screen>
+   $ export CVS_RSH=ssh
+   $ export CVSROOT=':ext:NAME@mitgcm.org:/u/gcmpack'
+   $ mkdir scratch
+   $ cvs co -P MITgcm manual mitgcm.org
+ </screen>
+       <para>These commands extract the necessary information from the CVS server
+       and create a temporary (called <filename>scratch</filename>) directory for
+       the storage of the HTML and other files that will be created.  Please note
+       that you must either create <filename>scratch</filename> as shown or edit
+       the various <filename>Makefile</filename>s and scripts used to create the
+       documentation.</para>
+     </sect2>
+     <sect2>
+       <title>Editing the Documentation</title>
+       <para>The documentation is contained in the <filename>manual</filename>
+       directory in a raw LaTeX format.  The main document is
+       <filename>manual.tex</filename> and it uses <command>\input{}</command>s
+       to include the chapters and subsections.</para>
+       <para>Since the same LaTeX source is used to produce PostScript, PDF, and
+       HTML output, care should be taken to follow certain conventions.  Two of
+       the most important are the usage of the <command>\filelink{}{}</command>
+       and <command>\varlink{}{}</command> commands.  Both of these commands have
+       been defined to simplify the connection between the automatically
+       generated ("code browser") HTML and the HTML version of the manual
+       produced by LaTeX2HTML.  They each take two arguments (corresponding to
+       the contents of the two sets of curly braces) which are the text that the
+       author wishes to be "wrapped" within the link, and a specially formatted
+       link thats relative to the <filename>MITgcm</filename> directory within
+       the CVS tree.</para>
+       <para>The result is a command that resembles either</para>
+       <orderedlist>
+         <listitem>
+           <para>a reference to a variable or subroutine name such as
+           <command>\varlink{tRef}{tRef}</command>, or </para>
+         </listitem>
+         <listitem>
+           <para>a reference to a file such as
+               <command>\varlink{tRef}{path-to-the-file_name.F}</command>
+               where the absolute path to the file is of the form
+               <filename>/foo/MITgcm/path/to/the/file_name.F</filename></para>
+               <para>(please note how the leading "/foo/MITgcm"
+               component of the path is dropped leaving the path
+               <emphasis>relative</emphasis> to the head of the code
+               directory and each directory separator "/" is turned
+               into a "-")</para>
+         </listitem>
+       </orderedlist>
+     </sect2>
+     <sect2>
+       <title>Building the Documentation</title>
+       <para>Given the directory structure of <xref
+       linkend="documentation_getting">, the entire documentation for the web
+       site can be built using:</para>
+ <screen>
+   $ cd mitgcm.org/devel/buildweb
+   $ make All
+ </screen>
+       <para>Which builds the PDF from the LaTeX source, creates the HTML output
+       from the LaTeX source, parses the FORTRAN code base to produce a
+       hyperlinked HTML version of the source, and then determines the
+       cross-linking between the various HTML components.</para>
+       <para>If there are no errors, the result of the build process (which can
+       take 30+ minutes on a P4/2.5Ghz) will be contained within a single
+       directory called <filename>scratch/dev_docs</filename>.  This is a freshly
+       built version of the entire on-line users manual.  If you have the correct
+       permissions, it can be directly copied to the web server area:</para>
+ <screen>
+   $ mv scratch/dev_docs /u/u0/httpd/html
+ </screen>
+       <para>and the update is complete.</para>
+     </sect2>
+   </sect1>
  </article>

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