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-revision 1.8 by jmc,
Wed Jan  5 03:45:24 2005 UTC
+revision 1.18 by jmc,
Tue Dec 19 18:38:40 2017 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>
+       <revision>
+         <revnumber>0.04</revnumber>
+         <date>2011-04-24</date>
+         <authorinitials>jmc</authorinitials>
+         <revremark>
+           Update subsection "The verification suite".
+         </revremark>
+       </revision>
      </revhistory>
      <abstract>
-Line 37
+Line 65
      <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 84
        <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 122
    <sect1 id="cvs">
      <title>CVS Repository</title>
      <sect2>
        <title>Layout</title>
-Line 104
+Line 133
        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 210
        <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 (login access) to the server
+            "mitgcm.org" (curently: <filename>forge.csail.mit.edu</filename>)
+            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
+            (we recommend to ask your senior MITgcm-collaborator to send such
+            request to marshall-admin at techsquare.com with Cc to Chris Hill
+            for approval).</para>
+           <para> The access to the server <filename>mitgcm.org</filename> 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 ssh to <filename>mitgcm.org</filename>
+            (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://mailman.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 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://mailman.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 CVS-anonymous mode (using "cvsanon",
+         as mentionned <ulink url="http://mitgcm.org/public/source_code.html">
+         here </ulink>) does not provide 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> The reason for such limitation is that when 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>.
+            This prevent 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>
+           <para> Note:
+            Please ignore the following warnings that the "cvs commit" command
+            produces if you are not part of the "gcmpack" group:
+ <screen>
+    cvs commit: failed to create lock directory for `/u/gcmpack/CVSROOT'
+    (/u/gcmpack/CVSROOT/#cvs.history.lock): Permission denied
+    cvs commit: failed to obtain history lock in repository `/u/gcmpack'
+ </screen>
+           These warnings are not affecting the changes you made to the CVS repository.
+           </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 343
          <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 359
              <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 253 
 checkpoint50e_post
+Line 380 
 checkpoint50e_post
  o make KPP work with PTRACERS
   - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
     nearly a copy of kpp_transport_s
   - there is no analogue to SurfaceTendencyS, so I have to use
     gPtr(of the surface layer) instead
  o add a new platform SunFire+mpi (SunFire 15000) to genmake
  checkpoint50e_pre
  checkpoint50d_post
  o change kpp output from multiple-record state files to single-record state
    files analogous to write_state.F
  o reduce the output frequency of cg3d-related stuff to the monitor frequency,
    analogous to the cg2d-related output.
  o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
    so that writing to internal file fn (with length 512) fails.
  checkpoint50d_pre
  </programlisting>
-Line 277 
 checkpoint50d_pre
+Line 404 
 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 417 
 checkpoint50d_pre
          For MITgcm, the process is similar.  Typical commands are:</para>
  <screen>
-   $ genmake -mods=../code
+   $ genmake2 -mods=../code
    $ make depend
    $ make
  </screen>
        <para>The following sections describe the individual steps in the build
          process.</para>
        <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 
 checkpoint50d_pre
+Line 485 
 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 544 
 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 
 checkpoint50d_pre
+Line 571 
 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>
                  <listitem><para>Packages either explicitly specified or
                      provided by default (in the order given)</para></listitem>
                  <listitem><para>Packages included due to package dependencies
                      (in the order that that package dependencies are
                      parsed)</para></listitem>
                  <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 639 
 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 652 
 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 661 
 checkpoint50d_pre
+Line 696 
 checkpoint50d_pre
              <listitem>
                <para>This target produces an <filename>mitgcmuv_ad</> executable
                  using the <filename>taf</> or <filename>staf</> adjoint
                  compiler.  See the <filename>genmake2</> "-adof" option for
                  compiler selection.</para>
              </listitem>
            </varlistentry>
-Line 687 
 checkpoint50d_pre
+Line 722 
 checkpoint50d_pre
        <title>The Verification Suite</title>
        <para>The MITgcm CVS tree (within the <filename>$ROOTDIR/verification/</>
-         directory) includes more than a dozen examples intended for regression
+         directory) includes many (> 90) examples intended for regression
-         testing.  Each one of these example directories contains "known-good"
+         testing.  Each one of these test-experiment directories contains "known-good"
          output files along with all the input (including both code and data
-         files) required for their re-calculation.  These example directories are
+         files) required for their re-calculation.
-         further broken down into sets of subdirectories
+         Also included in <filename>$ROOTDIR/verification/</> is the shell
-         (eg. <filename>/input</>, <filename>/code</>) intended to expedite the
+         script <filename>testreport</> to perform regression tests.</para>
-         testing process.</para>
+       <sect3 id="test-experiment">
+         <title>Test-experiment Directory Content</title>
+           <para> Each test-experiment directory (<filename>TESTDIR</>) contains
+           several standard subdirectories and files which <filename>testreport</>
+           recognizes and uses when running a regression test.
+           The directories/files that <filename>testreport</> uses are different
+           for a forward test and an adjoint test (<filename>testreport -adm</>)
+           and some test-experiments are set-up for only one type of regression
+           test whereas others allow both types of tests (forward and adjoint).</para>
+           <para>Also some test-experiment allows, using the same MITgcm executable,
+           to perform multiple tests using different parameters and input files,
+           with a primary input set-up
+           (<filename>input/ </> or <filename>input_ad/ </>)
+           and corresponding results (<filename>results/output.txt</> or
+           <filename>results/output_adm.txt</>) and with one or several secondary
+           inputs (<filename>input.OTHER/ </> or <filename>input_ad.OTHER/ </>)
+           and corresponding results (<filename>results/output.OTHER.txt </>
+           or <filename>results/output_adm.OTHER.txt</>).</para>
+         <variablelist>
+           <varlistentry>
+             <term>directory <filename>TESTDIR/results/</></term>
+             <listitem>
+               <para>contains reference standard output used for test comparison.
+                 <filename>results/output.txt</> and
+                 <filename>results/output_adm.txt</>
+                 correspond respectively to primary forward and adjoint test
+                 run on the reference platform (currently
+                 <filename>baudelaire.csail.mit.edu</>)
+                 on one processor (no MPI, single thread)
+                 using the reference compiler (curently the GNU fortran
+                 compiler <filename>gfortran</>).
+                 The presence of these files determines whether or not
+                 <filename>testreport</> is testing or skipping
+                 this test-experiment.
+                 Reference standard output for secondary tests
+                 (<filename>results/output.OTHER.txt</>
+                 or <filename>results/output_adm.OTHER.txt</>) are
+                 also expected here.</para>
+               <para>The test comparison involves few model variables output, which are,
+                 by default and for a forward test, the 2-D solver initial residual
+                 (<filename>cg2d_init_res</>) and 3-D state variables (T,S,U,V)
+                 monitor output, and, by default and for an adjoint test, the
+                 cost-function and gradient-check. However, some test-experiments
+                 use some package-specific variable/monitor output according to
+                 the file <filename>TESTDIR/input[_ad][.OTHER]/tr_checklist</>
+                 specification.</para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term>directory <filename>TESTDIR/build/</></term>
+             <listitem>
+               <para> initially empty directory where <filename>testreport</>
+                 will build the MITgcm executable for forward and adjoint test.
+                 It might contains an experiment specific
+                 <filename>genmake_local</> file (see <xref linkend="genmake">).
+                 </para>
+               <para> Note that the original <filename>code[_ad]/SIZE.h_mpi</>
+                 is not directly used as "SIZE.h" to build an MPI-executable ;
+                 instead, a local copy <filename>build/SIZE.h.mpi</> is derived
+                 from <filename>code[_ad]/SIZE.h_mpi</>
+                 by adjusting the number of processors (nPx,nPy) according to
+                 <filename>NUMBER_OF_PROCS</> (see <xref linkend="testreport">,
+                 <filename>testreport -MPI</>) ; then it is linked to "SIZE.h"
+                 (<filename> ln -s SIZE.h.mpi SIZE.h </>) before building
+                 the MPI-executable.</para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term>directory <filename>TESTDIR/code/</></term>
+             <listitem>
+               <para>contains the test-experiment specific source code
+                 used to build the MITgcm executable (<filename>mitgcmuv</>)
+                 for forward-test (using <filename>genmake2 -mods=../code</>).
+                 </para>
+                 <para> It can also contain specific source files with the suffix
+                 "<filename>_mpi</>" to be used
+                 <!--
+                 in the <filename>TESTDIR/build/</> directory
+                 -->
+                 in place of the corresponding file (without suffix)
+                 for an MPI test (see <xref linkend="testreport">).
+                 The presence or absence of <filename>SIZE.h_mpi</>
+                 determines whether or not an MPI test on this
+                 test-experiment is performed or skipped.</para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term>directory <filename>TESTDIR/code_ad/</></term>
+             <listitem>
+               <para>contains the test-experiment specific source code
+                 used to build the MITgcm executable (<filename>mitgcmuv_ad</>)
+                 for adjoint-test (using <filename>genmake2 -mods=../code_ad</>).
+                 It can also contain specific source files with the suffix
+                 "<filename>_mpi</>" (see above).</para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term>directory <filename>TESTDIR/input/</></term>
+             <listitem>
+               <para>contains the input and parameter files
+                 used to run the primary forward test of this test-experiment.
+                 </para>
+               <para>It can also contain specific parameter files with the suffix
+                 "<filename>.mpi</>" to be used
+                 <!--
+                 in the <filename>TESTDIR/run/</> directory
+                 -->
+                 in place of the corresponding file (without suffix) for MPI
+                 test, or with suffix "<filename>.mth</>" to be used for
+                 multi-threaded test (see <xref linkend="testreport">).
+                 The presence or absence of <filename>eedata.mth</>
+                 determines whether or not a multi-threaded test on this
+                 test-experiment is performed or skipped.</para>
+               <para>To save disk space and reduce downloading time, multiple
+                 copies of the same input file is avoided by using a shell
+                 script <filename>prepare_run</>.
+                 When such a script is found in <filename>TESTDIR/input/ </>,
+                 <filename>testreport</> run this script in directory
+                 <filename>TESTDIR/run/ </> after linking all the input file
+                 from <filename>TESTDIR/input/ </>.
+                 </para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term>directory <filename>TESTDIR/input_ad/</></term>
+             <listitem>
+               <para>contains the input and parameter files
+                 used to run the primary adjoint test of this test-experiment.
+                 It can also contain specific parameter files with the suffix
+                 "<filename>.mpi</>" and shell script <filename>prepare_run</>
+                 as described above.</para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term>directory <filename>TESTDIR/input.OTHER/</></term>
+             <listitem>
+               <para>contains the input and parameter files
+                 used to run the secondary OTHER forward test of this test-experiment.
+                 It can also contain specific parameter files with suffix
+                 "<filename>.mpi</>" or "<filename>.mth</>" and shell script
+                 <filename>prepare_run</> (see above).</para>
+                 <para> The presence or absence the file <filename>eedata.mth</>
+                 determines whether or not a secondary multi-threaded test on this
+                 test-experiment is performed or skipped.</para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term>directory <filename>TESTDIR/input_ad.OTHER/</></term>
+             <listitem>
+               <para>contains the input and parameter files
+                 used to run the secondary OTHER adjoint test of this test-experiment.
+                 It can also contain specific parameter files with the suffix
+                 "<filename>.mpi</>" and shell script <filename>prepare_run</>
+                 (see above).</para>
+             </listitem>
+           </varlistentry>
+                 <!--
+                 -->
+           <varlistentry>
+             <term>directory <filename>TESTDIR/run/</></term>
+             <listitem>
+               <para> initially empty directory where <filename>testreport</>
+                 will run the MITgcm executable for primary forward and adjoint
+                 test.</para>
+               <para>Symbolic links (using command "<filename>ln -s</>") are made
+                 for input and parameter files (from <filename>../input/ </>
+                 or from <filename>../input_ad/ </>) and for MITgcm executable
+                 (from <filename>../build/ </>) before the run proceeds.
+                 The sequence of links (function <filename>linkdata</> within shell
+                 script <filename>testreport</>) for a forward test is:</para>
+ <screen>
+ * link+rename or remove links
+        to special files with suffix ".mpi" or ".mth" from ../input/
+ * link files from ../input/
+ * execute ../input/prepare_run (if it exists)
+ </screen>
+               <para>The sequence for an ajoint test is similar, with
+                 <filename>../input_ad/ </> replacing <filename>../input/ </>.
+                 </para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term>directory <filename>TESTDIR/tr_run.OTHER/</></term>
+             <listitem>
+               <para> directory created by <filename>testreport</>
+                 to run the MITgcm executable for secondary "OTHER" forward
+                 or adjoint test.</para>
+               <para> The sequence of links for a forward secondary test is:</para>
+ <screen>
+ * link+rename or remove links
+        to special files with suffix ".mpi" or ".mth" from ../input.OTHER/
+ * link files from ../input.OTHER/
+ * execute ../input.OTHER/prepare_run (if it exists)
+ * link files from ../input/
+ * execute ../input/prepare_run (if it exists)
+ </screen>
+               <para>The sequence for an ajoint test is similar, with
+                 <filename>../input_ad.OTHER/ </> and <filename>../input_ad/ </>
+                 replacing <filename>../input.OTHER/ </> and <filename>../input/ </>.
+                 </para>
+             </listitem>
+           </varlistentry>
+         </variablelist>
+       </sect3>
        <sect3 id="testreport">
          <title>The <filename>testreport</> Utility</title>
-         <para>Also included in <filename>$ROOTDIR/verification/</> are shell
+         <para> The shell script  <filename>testreport</> (in
-           scripts for automated testing.  The newest script (which was written
+           <filename>$ROOTDIR/verification/</>), which was written to work with
-           to work with <filename>genmake2</>) is called <filename>testreport</>.
+           <filename>genmake2</>, can be used to build different versions
-           This script can be used to build different versions of the MITgcm
+           of the MITgcm code, run the various examples, compare the output,
-           code, run the various examples, compare the output, and (if specified)
+           and (if specified) email the results of each one of these tests to a
-           email the results of each one of these tests to a central
+           central repository.</para>
-           repository.</para>
          <para>On some systems, the testreport script can be run with a command
          line as simple as:</para>
  <screen>
    $ cd verification
-   $ ./testreport -ieee
+   $ ./testreport
  </screen>
          <para>However, some systems (those lacking or wiht a broken "/bin/sh")
            may require an explicit shell invocation such as:</para>
  <screen>
-   $ sh ./testreport -ieee -t 'exp0 exp4'
+   $ sh ./testreport -t 'exp2 exp4'
-   $ /some/path/to/bash ./testreport -ieee -t 'ideal_2D_oce lab_sea natl_box'
+   $ /some/path/to/bash ./testreport -t 'ideal_2D_oce lab_sea natl_box'
  </screen>
          <para>The <filename>testreport</> script accepts a number of
-Line 729 
 checkpoint50d_pre
+Line 978 
 checkpoint50d_pre
          <variablelist>
            <varlistentry>
-             <term><filename>-ieee</></term>
+             <term><filename>-ieee</> (default) / <filename>-noieee</></term>
              <listitem>
                <para>If allowed by the compiler (as defined in the "optfile"),
-                 use IEEE arithmetic.  This option, along with the GCC compiler,
+                 use IEEE arithmetic (<filename>genmake2 -ieee</>).
-                 is how the standard results were produced.</para>
+                 This option, along with the gfortran / gcc compiler,
+                 is how the standard results are produced.</para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term><filename>-optfile=/PATH/FILENAME</></term>
+             <term><filename>-optfile '/PATH/F1 [/PATH/F2 ...]'</></term>
+             <listitem>
+               <para>This specifies a list of "options files" that will be passed
+                 to <filename>genmake2</>.  If multiple options files are used
+                 (say, to test different compilers or different sets of options
+                 for the same compiler), then each options file will be used with
+                 each of the test directories.</para>
              </listitem>
            </varlistentry>
-Line 744 
 checkpoint50d_pre
+Line 1006 
 checkpoint50d_pre
                <para>This option specifies the test directory or list of test
                  directories that should be used.  Each of these entries should
                  exactly (note: they are case sensitive!) match the names of
-                 directries in <filename>$ROOTDIR/verification/</>.  If this
+                 directories in <filename>$ROOTDIR/verification/</>.  If this
                  option is omitted, then all directories that are properly
                  formatted (that is, containing an <filename>input</>
                  sub-directory and a <filename>results/output.txt</> file) will
-Line 753 
 checkpoint50d_pre
+Line 1015 
 checkpoint50d_pre
            </varlistentry>
            <varlistentry>
-             <term><filename>-optfile=/PATH/FILENAME</></term>
-             <term><filename>-optfile '/PATH/F1 [/PATH/F2 ...]'</></term>
-             <listitem>
-               <para>This specifies a list of "options files" that will be passed
-                 to <filename>genmake2</>.  If multiple options files are used
-                 (say, to test different compilers or different sets of options
-                 for the same compiler), then each options file will be used with
-                 each of the test directories.</para>
-             </listitem>
-           </varlistentry>
-           <varlistentry>
              <term><filename>-addr EMAIL</></term>
              <term><filename>-addr 'EMAIL1 EMAIL2 [...]'</></term>
              <listitem>
-Line 778 
 checkpoint50d_pre
+Line 1028 
 checkpoint50d_pre
            </varlistentry>
            <varlistentry>
+             <term><filename>-MPI NUMBER_OF_PROCS</></term>
              <term><filename>-mpi</></term>
              <listitem>
-               <para>If the necessary files
+               <para>If the necessary file (<filename>TESTDIR/code/SIZE.h_mpi</>)
-               (<filename>TESTDIR/code/CPP_EEOPTIONS.h_mpi</> and
+               exists, then use it (and all <filename>TESTDIR/code/*_mpi</> files)
-               <filename>TESTDIR/code/SIZE.h_mpi</>) exist, then use them for an
+               for an MPI--enabled run.  The new option (<filename>-MPI</> followed
-               MPI--enabled run.  Note that the use of MPI typically requires a
+               by the maximum number of processors) enable to build and run each
+               test-experiment using variable number of MPI processors (multiple
+               of <filename>nPx*nPy</> from <filename>TESTDIR/code/SIZE.h_mpi</>
+               and not larger than <filename>NUMBER_OF_PROCS</>).
+               The short option ("-mpi") can only be used to build and run on 2 MPI
+               processors (equivalent to "<filename>-MPI 2</>").</para>
+               <para>Note that the use of MPI typically requires a
                special command option (see "-command" below) to invoke the MPI
-               executable.  Examples of PBS scripts using MPI with testreport can be
+               executable.  Examples of PBS scripts using testreport with MPI 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/tools/example_scripts/">
-               MITgcm-contrib area</ulink></para>
+               tools/example_scripts directory</ulink>.</para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term><filename>-command='some command to run'</></term>
              <listitem>
-               <para>For some tests, particularly MPI runs, the default "make
+               <para>For some tests, particularly MPI runs, a specific command
-               output.txt" is not sufficient.  This option allows a more general
+               might be needed to run the executable. 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
+               using testreport with MPI 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/tools/example_scripts/">
-               MITgcm-contrib area</ulink></para>
+               tools/example_scripts directory</ulink>.</para>
+               <para>
+                 For the case where the number of MPI processors varies according
+                 to each test-experiment, some key-words within the command-to-run
+                 argument will be replaced by their effective value:</para>
+               <para>
+                 <filename>TR_NPROC </> will be replaced by the actual number
+                 of MPI processors needed to run the current test-experiment.</para>
+               <para>
+                 <filename>TR_MFILE </> will be replaced by the name of local-file
+                 that testreport creates from the full list of machines which
+                 "<filename>testreport -mf MACHINE_FILE</>" provides, but truncated
+                 to the exact number of machines.</para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term><filename>-mf MACHINE_FILE</></term>
+             <listitem>
+               <para>
+                 To use with <filename>-MPI NUMBER_OF_PROCS</> option, to specify
+                 the file containing the full list of <filename>NUMBER_OF_PROCS</>
+                 machines to use for the MPI runs.</para>
+             </listitem>
+           </varlistentry>
+           <varlistentry>
+             <term><filename>-mth</></term>
+             <listitem>
+               <para>compile (with <filename>genmake2 -omp</>) and run with
+                 multiple threads (using eedata.mth).</para>
              </listitem>
            </varlistentry>
          </variablelist>
-         <para>The <filename>testreport</> script will write progress to the
+         <para>The <filename>testreport</> script will create an output directory
-           screen (stdout) as it runs.  In addition, it will create a
+           <filename>tr_NAME_DATE_N/ </>, with <filename>hostname</> as default
-           <filename>tr_out.txt</> file that contains a brief comparison of the
+           <filename>NAME</>, <filename>DATE</> the current date followed by
-           current output with the "known-good" output.</para>
+           a suffix number "N" to distinguish from previous
+           <filename>testreport</> output directories.
+           <filename>testreport</> writes progress to the screen (stdout)
+           and reports into the ouput directory as it runs.
+           In particular, one can find, in the ouput directory,
+           the <filename>summary.txt</> file that contains a brief comparison
+           of the current output with the "known-good" output.
+           At the end of the testing process, the <filename>tr_out.txt</> file
+           is generated in <filename>$ROOTDIR/verification/ </>
+           as a compact version of <filename>summry.txt</> file.</para>
        </sect3>
+       <sect3 id="tst_2plus2">
+         <title>The <filename>do_tst_2+2</> Utility</title>
+         <para> The shell script  <filename>do_tst_2+2</> (in
+           <filename>$ROOTDIR/tools/ </>)
+           can be used to check the accuracy of the restart procedure.
+         </para>
+       </sect3>
      </sect2>
-Line 826 
 checkpoint50d_pre
+Line 1130 
 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 851 
 separated from the generic fluid dynamic
+Line 1155 
 separated from the generic fluid dynamic
  below using generic package names ${pkg}.
  A concrete examples of a package is the code
  for implementing GM/Redi mixing. This code uses
  the package name
  *   ${PKG} = GMREDI
  *   ${pkg} = gmredi
  *   ${Pkg} = gmRedi
-Line 886 
 o  Each package gets its runtime configu
+Line 1190 
 o  Each package gets its runtime configu
     Package runtime config. options are imported
     into a common block held in a header file
     called "${PKG}.h".
     Note: In some packages, the header file "${PKG}.h" is splitted
     into "${PKG}_PARAMS.h" that contains the package parameters and
     ${PKG}_VARS.h" for the field arrays.
  o  The core driver part of the model can check
-Line 911 
 CPP Flags
+Line 1215 
 CPP Flags
 . Within the core driver code flags of the form
         ALLOW_${PKG} are used to include or exclude
         whole packages. The ALLOW_${PKG} flags are included
         from a PACKAGES_CONFIG.h file that is automatically
         generated by genmake2 (see genmake2 section).
         held in-line in the CPP_OPTIONS.h header file.
         e.g.
-Line 930 
 CPP Flags
+Line 1234 
 CPP Flags
 . Within an individual package a header file,
         "${PKG}_OPTIONS.h", is used to set CPP flags
         specific to that package. It also includes
         "PACKAGES_CONFIG.h" and "CPP_OPTIONS.h".
-Line 944 
 Package Boot Sequence
+Line 1248 
 Package Boot Sequence
 . S/R PACKAGES_BOOT()
              :
          CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... )
 . S/R PACKAGES_READPARMS()
              :
-Line 983 
 Package Output
+Line 1287 
 Package Output
          #ifdef ALLOW_${PKG}
            if ( use${Pkg} )
-      &       CALL ${PKG}_DIAGS( )     [ or CALL ${PKG}_OUTPUT( ) ]
+      &       CALL ${PKG}_OUTPUT( )
          #endif
 . S/R PACKAGES_WRITE_PICKUP()
-Line 996 
 Package Output
+Line 1300 
 Package Output
  Description
  ===========
        - ${PKG}_READPARMS()
      is responsible for reading
      in the package parameters file data.${pkg}, and storing
      the package parameters in "${PKG}.h" (or in "${PKG}_PARAMS.h").
      -> called from INITIALISE_FIXED in PACKAGES_READPARMS
       - ${PKG}_INIT_FIXED()
      is responsible for completing the internal setup of a package.
      -> called from INITIALISE_FIXED in PACKAGES_INIT_FIXED
      note: 1) some pkg use instead:
               CALL ${PKG}_INITIALISE  ( or the old form CALL ${PKG}_INIT )
 ) for simple pkg setup, this part is done inside ${PKG}_READPARMS
       - ${PKG}_CHECK()
      is responsible for validating
      basic package setup and inter-package dependencies.
      ${PKG}_CHECK can import other package parameters it may
-Line 1018 
 Description
+Line 1322 
 Description
      will not be reset during ${PKG}_CHECK().
      -> called from INITIALISE_FIXED in PACKAGES_CHECK
       - ${PKG}_INIT_VARIA()
      is responsible for fill-in all package variables with an initial value.
      Contains eventually a call to ${PKG}_READ_PICKUP that will read
      from a pickup file the package variables required to restart the model.
      This routine is called after the core model state has been completely
      initialised but before the core model timestepping starts.
      -> called from INITIALISE_VARIA in PACKAGES_INIT_VARIABLES
      note: the name ${PKG}_INIT_VARIA is not yet standard and some pkg
       use for e.g. ${PKG}_INI_VARS, ${PKG}_INIT_VARIABLES, or the old
       form ${PKG}_INIT
-      - ${PKG}_DIAGS()      [or ${PKG}_OUTPUT( ) ]
+      - ${PKG}_OUTPUT( )
       is responsible for writing time-average fields to output files
       (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: 1) ${PKG}_OUTPUT is progressively replacing ${PKG}_DIAGS()
+      NOTE: 1) the S/R old name ${PKG}_DIAGS is used in some packages
+               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()
       is responsible for writing a package pickup file when necessary for
       a restart. (found also the old name: ${PKG}_WRITE_CHECKPOINT )
      -> called from FORWARD_STEP and THE_MODEL_MAIN in PACKAGES_WRITE_PICKUP
-Line 1075 
 Summary
+Line 1380 
 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 output to file.
+   * ${pkg}_output.F       write output to file.
-    or ${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
-Line 1091 
 Summary
+Line 1395 
 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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