MITgcm/doc/devel_HOWTO.sgml

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<article id="MITgcm-Development-HOWTO">

  <articleinfo>
    <title>MITgcm Development HOWTO</title>

    <author>
      <firstname>Ed</firstname>
      <surname>Hill III</surname>
      <affiliation>
        <address><email>eh3@mit.edu</email></address>
      </affiliation>
    </author>

    <revhistory>
      <revision>
	<revnumber>0.01</revnumber>
	<date>2003-08-07</date>
	<authorinitials>eh3</authorinitials>
	<revremark>
	  Initial version.
        </revremark>
      </revision>
      <revision>
	<revnumber>0.02</revnumber>
	<date>2010-01-21</date>
	<authorinitials>jmc</authorinitials>
	<revremark>
	  update links.
        </revremark>
      </revision>
    </revhistory>

    <abstract>
      <para>This document describes how to develop software for the
      MITgcm project.</para>
    </abstract>
  </articleinfo>

  <sect1 id="intro">
    <title>Introduction</title> <para>The purpose of this document is
    to help new developers get "up to speed" with MITgcm
    development.</para>
    <sect2>
      <title>New Versions of This Document</title> <para>You can
      obtain the latest version of this document <ulink
      url="http://mitgcm.org/public/docs.html">online</ulink> in
      various formats.</para>
    </sect2>
    <sect2>
      <title>Feedback and corrections</title> <para>If you have
      questions or comments about this document, please feel free to
      <ulink url="mailto:MITgcm-support@mitgcm.org">contact the
      authors</ulink>.
      </para>
    </sect2>
  </sect1>

  <sect1 id="background">
    <title>Background</title>

    <sect2>
      <title>User Manual</title>

      <para>Before jumping into development, please familiarize yourself with
	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>

      <!--
      <para>Also, a "snapshot" or <ulink
      url="http://mitgcm.org/dev_docs/">development version</ulink> of
      the user manual may be available, though this is only put on the
      web for testing purposes.</para>
      -->
    </sect2>

    <sect2>
      <title>Prerequisites</title> <para>To develop for MITgcm project
      you will need a UNIX or UNIX-like set of build tools including
      the following:</para>
      <blockquote>
	<simplelist type="inline">
	  <member>CVS client</member>
	  <member>make or (preferably) GNU make</member>
	  <member>FORTRAN compiler</member>
	  <member>C compiler</member>
	  <member>[ba]sh and [t]csh shells</member>
	  <member>PERL</member>
	  <member>LaTeX and LaTeX2HTML</member>
	</simplelist>
      </blockquote>
      <para>Essentially all of the work described here has been tested
      on recent versions of Red Hat Linux (eg. 7.3 through 9).  Except
      where noted, all shell commands will be provided using bash
      syntax.
      </para>
    </sect2>

  </sect1>

  <sect1 id="cvs">
    <title>CVS Repository</title>
    <sect2>
      <title>Layout</title>

      <para>Unlike many open source projects, the MITgcm CVS tree does
      not follow a simple "src", "docs", "share", and "test" directory
      layout.  Instead, there are multiple higher-level directories
      that each, to some extent, depend upon the presence of the
      others.  The tree currently resembles:</para>

<programlisting>gcmpack/
  MITgcm-contrib        contributed code
  CS-regrid             goes into utils
  cvspolicy.html        -save-
  CVSROOT               -save-
  development           experimental stuff
  manual                -save-
  misc                  -?-

  MITgcm                code
       adjoint                  fold into genmake
       bin                      stub for ecco build
       compare01                old from 20th century
       diags                    timeave f77 in pkgs now
       doc                      tags -- connect to real docs?
       eesupp                   cnh?
       exe                      ecco user build
    ,- jobs                     runtime shell scripts for 
    |                             various platforms
    |  lsopt                    line search
   m|  model                    main dynamics (core)
   e|    optimization_drivers   ?
   r|  optim                    line search interface
   g|  pkg                      alternate and optional numerics, etc.
   e|- tools
   ?|  tutorial_examples        documented tests
    |                             only populated on release1 branch 
    |                             and not validated during "testreport"
    '- utils
       verification             std tests


  mitgcmdoc -> manual   -remove-
  mitgcm.org            build web site
  models                -?-
  packages              -?-
  preprocess            -?-
  tmp                   -?-
</programlisting>

      <para>Efforts are underway to reduce the complexity.</para>

    </sect2>

 <!--
    <sect2>
      <title>Releases</title> <para>Currently, there are two main
      branches:</para>
      <itemizedlist mark="bullet">
        <listitem>
          <para>Development</para>
	  <itemizedlist mark="bullet">
	    <listitem>
	      <para>MAIN</para>
	    </listitem>
	    <listitem>
	      <para>ecco-branch</para>
	    </listitem>
	  </itemizedlist>
        </listitem>
        <listitem>
          <para>Production</para>
	  <itemizedlist mark="bullet">
	    <listitem>
	      <para>Release1</para>
	    </listitem>
	    <listitem>
	      <para>Release2</para>
	    </listitem>
	  </itemizedlist>
        </listitem>
      </itemizedlist>
    </sect2>
-->

    <sect2>
      <title>Branches</title>

      <para>As shown in the online <ulink
      url="http://mitgcm.org/viewvc/MITgcm/MITgcm/doc/tag-index?view=graph">
      ViewCVS-generated tree</ulink>, the MITgcm codebase is split into to two
      branches or "lines" under which development proceeds.  These two lines are
      referred to as the "MAIN" and "ecco" versions of the code.  While not
      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.
      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>
    </sect2>

    <sect2>
      <title>Tagging</title>

      <para>The intent of tagging is to create "known-good" checkpoints that
      developers can use as references.  Traditionally, MITgcm tagging has
      maintained the following conventions:</para>

      <orderedlist>
	<listitem>
	  <para>Developer checks out code into a local CVS-managed directory,
	  makes various changes/additions, tests these edits, and eventually
	  reaches a point where (s)he is satisfied that the changes form a new
	  "useful" point in the evolution of the code.</para>
	</listitem>

	<listitem>
	  <para>The developer then runs the <ulink
          url="http://mitgcm.org/viewvc/MITgcm/MITgcm/verification/testreport">
          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.
          </para>
	</listitem>

	<listitem>
	  <para>Having satisfied him- or herself that the changes are
	  ready to be committed to the CVS repository, the developer
	  then:</para>
	  <orderedlist>
	    <listitem>
	      <para>adds a "checkpointXY_pre" comment (where X is a checkpoint
	      number and Y is a letter) to the <ulink
	      url="http://mitgcm.org/viewvc/MITgcm/MITgcm/doc/tag-index">
	      tag-index</ulink> file and checks it into the CVS
	      repository</para>
	    </listitem>
	    <listitem>
	      <para>submits the set of changes to the CVS repository and adds
	      comments to <filename>tag-index</filename> describing what the
	      changes are along with a matching "checkpointXY_post" entry</para>
	    </listitem>
	  </orderedlist>
	</listitem>
      </orderedlist>

      <para>The result of this tagging procedure is a sequence of development
      checkpoints with comments which resembles:</para>

<programlisting>
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>

      <para>This information can be used to refer to various stages of the code
      development.  For example, bugs can be traced to individual sets of CVS
      checkins based upon their first appearance when comparing the results from
      different checkpoints.</para>

    </sect2>
  </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>

  <sect1 id="coding">
    <title>Coding for MITgcm</title>

    <sect2 id="build_tools">
      <title>Build Tools</title>

      <para>Many Open Source projects use the "GNU Autotools" to help streamline
	the build process for various Unix and Unix-like architectures.  For a
	user, the result is the common "configure" (that is,
	"<filename>./configure && make && make install</filename>") commands.
	For MITgcm, the process is similar.  Typical commands are:</para>

<screen>
  $ genmake -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
	    deprecated and will eventually be replaced by <filename>genmake2</>.
	    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
	  <filename>make</filename> to specify how to compile the MITgcm source
	  files.  For more detailed descriptions of what the make tools are and
	  how they are used, please see:</para>

	<itemizedlist>
	  <listitem>
	    <para><ulink url="http://www.gnu.org/software/make/make.html">
		http://www.gnu.org/software/make/make.html</></para>
	  </listitem>
	  <listitem>
	    <para><ulink url="http://www.oreilly.com/catalog/make2/">
		http://www.oreilly.com/catalog/make2/</></para>
	  </listitem>
	</itemizedlist>

	<para>Genmake can often be invoked successfully with a command line as
	simple as:</para>

<screen>
  $ genmake2 -mods=../code
</screen>

	<para>However, some systems (particularly commercial Unixes that lack a
	  more modern "/bin/sh" implementation or that have shells installed in
	  odd locations) may require an explicit shell invocation such as one of
	  the following: </para>

<screen>
  $ /usr/bin/sh genmake2 -make=gmake  -mods=../code
  $ /opt/gnu/bin/bash genmake2 -ieee -make=/usr/local/bin/gmake -mods=../code
</screen>

	<para>The genmake2 code has been written in a Bourne and BASH (v1)
	compatible syntax so it should work with most "sh" and all recent "bash"
	implementations.</para>

	<para>As the name implies, <filename>genmake2</filename> generates a
	  <filename>Makefile</filename>.  It does so by first parsing the
	  information supplied from the following sources</para>

	<orderedlist>
	  <listitem>
	    <para>a <filename>gemake_local</filename> file in the current
	      directory</para>
	  </listitem>
	  <listitem>
	    <para>directly from command-line options</para>
	  </listitem>
	  <listitem>
	    <para>an "options file" as specified by the command-line option
	      <filename>-optfile='FILENAME'</filename></para>
	  </listitem>
	</orderedlist>

	<para>then checking certain dependency rules (the package dependencies),
	  and finally writing a <filename>Makefile</filename> based upon the
	  source code that it finds.  For convenience within various Unix
	  shells, <filename>genmake2</> supports both "long"- and "short"-style
	  options.  A complete list of the available options can be obtained
	  from:</para>

<screen>
  $ genmake2 -help
</screen>

	<para>The most important options for <filename>genmake2</> are:</para>

	<variablelist>

	  <varlistentry>
	    <term><filename>--optfile=/PATH/FILENAME</></term>

	    <listitem>
	      <para>This specifies the "options file" that should be used for a
		particular build.  The options file is a convenient and
		machine-indepenent way of specifying parameters such as the
		FORTRAN compiler (<filename>FC=</>), FORTRAN compiler
		optimization flags (<filename>FFLAGS=</>), and the locations of
		various platform- and/or machine-specific tools
		(eg. <filename>MAKEDEPEND=</>).  As with <filename>genmake2</>,
		all options files should be written to be compatible with
		Bourne--shell ("sh" or "BASH v1") syntax.  Examples of various
		options files can be found in
		<filename>$ROOTDIR/tools/build_options</>.</para>

	      <para>If no "optfile" is specified (either through the command lin
		or the environment variable), genmake2 will try to make a
		reasonable guess from the list provided in
		<filename>$ROOTDIR/tools/build_options</>.  The method used for
		making this guess is to first determine the combination of
		operating system and hardware (eg. "linux_ia32") and then find a
		working Fortran compiler within the user's path.  When these
		three items have been identified, genmake2 will try to find an
		optfile that has a matching name. </para>

	      <para>Everyone is encouraged to submit their options files to the
		MITgcm project for inclusion (please send to
		<email>MITgcm-support@mitgcm.org</email>).  We are particularly
		grateful for options files tested on new or unique
		platforms!</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>

	  <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>
	      <para>This option specifies the "adjoint" or automatic
		differentiation options file to be used.  The file is analogous
		to the "optfile" defined above but it specifies information for
		the AD build process.  The default file is located in <filename>
		$ROOTDIR/tools/adjoint_options/adjoint_default </> and it
		defines the "TAF" and "TAMC" compilers.  An alternate version is
		also available at <filename>
		$ROOTDIR/tools/adjoint_options/adjoint_staf </> that selects the
		newer "STAF" compiler.  As with any compilers, it is helpful to
		have their directories listed in your $PATH environment
		variable.</para>
	    </listitem>
	  </varlistentry>

	  <varlistentry>
	    <term><filename>-mods=DIR</></term>
	    <term><filename>-mods='DIR1 [DIR2 ...]'</></term>
	    <listitem>
	      <para>This option specifies a list of directories containing
		"modifications".  These directories contain files with names
		that may (or may not) exist in the main MITgcm source tree but
		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>-make=/path/to/gmake</></term>
	    <listitem>
	      <para>Due to the poor handling of soft-links and other bugs common
		with the <filename>make</> versions provided by commercial Unix
		vendors, GNU <filename>make</filename> (sometimes called
		<filename>gmake</filename>) should be preferred.  This option
		provides a means for specifying the make program to be
		used.</para>
	    </listitem>
	  </varlistentry>

	</variablelist>
	
	<para>A successful run of <filename>genmake2</> will produce a
	  <filename>Makefile</>, a <filename>PACKAGES_CONFIG.h</> file, and
	  various convenience files used for the automatic differentiation
	  process.</para>

	<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
	  makefile".</para>

      </sect3>

      <sect3 id="makefile_use">
	<title>Using the <filename>Makefile</></title>

	<para>Once a <filename>Makefile</> has been created using
	  <filename>genmake2</>, one can build a "standard" (forward
	  simulator) executable using:</para>

<screen>
  $ make CLEAN
  $ make depend
  $ make
</screen>

	<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
	  the build.</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
	  parses these files and creates an extensive list of dependencies
	  within the <filename>Makefile</> itself.  The links that exist at this
	  stage are mostly "large F" files (*.F and *.F90) that need to be
	  processed by a C preprocessor ("CPP").  Since "make depend" edits the
	  <filename>Makefile</>, it is important not to skip this step!</para>

	<para>The final "make" invokes the C preprocessor to produce the "little
	  f" files (*.f and *.f90) and then compiles them to object code using
	  the specified FORTRAN compiler and options.  An intermediate script is
	  often used during this stage to further process (usually, make simple
	  substitutions) custom definitions such as variable types within the
	  source files.  This additional stage is necessary in order to overcome
	  some of the inconsistencies in the sizes of objects (bytes) between
	  different compilers. The result of the build process is an executable
	  with the name <filename>mitgcmuv</>.</para>

	<para>In addition to the forward simulator described above, the
	  <filename>Makefile</> also has a number of targets that can be used to
	  produce various adjoint and tangent-linear builds for optimization and
	  other parameter-sensitivity problems.  The additional targets within
	  the <filename>Makefile</> are:</para>

	<variablelist>

	  <varlistentry>
	    <term><filename>make adall</></term>
	    <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>

	  <varlistentry>
	    <term><filename>make ftlall</></term>
	    <listitem>
	      <para>Similar to <filename>make adall</> above, this
		produces...</para>
	    </listitem>
	  </varlistentry>

	</variablelist>

	<para>Please report any compilation failures or other build problems to
	  the <email>MITgcm-support@mitgcm.org</email> list.</para>

      </sect3>

    </sect2>

    <sect2 id="verification">
      <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
	testing.  Each one of these example 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
	further broken down into sets of subdirectories
	(eg. <filename>/input</>, <filename>/code</>) intended to expedite the
	testing process.</para>

      <sect3 id="testreport">
	<title>The <filename>testreport</> Utility</title>

	<para>Also included in <filename>$ROOTDIR/verification/</> are shell
	  scripts for automated testing.  The newest script (which was written
	  to work with <filename>genmake2</>) is called <filename>testreport</>.
	  This script can be used to build different versions of the MITgcm
	  code, run the various examples, compare the output, and (if specified)
	  email the results of each one of these tests to a central
	  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
</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'
  $ /some/path/to/bash ./testreport -ieee -t 'ideal_2D_oce lab_sea natl_box'
</screen>

	<para>The <filename>testreport</> script accepts a number of
	  command-line options which can be listed using the <filename>-help</>
	  option.  The most important ones are:</para>

	<variablelist>

	  <varlistentry>
	    <term><filename>-ieee</></term>
	    <listitem>
	      <para>If allowed by the compiler (as defined in the "optfile"),
		use IEEE arithmetic.  This option, along with the GCC compiler,
		is how the standard results were produced.</para>
	    </listitem>
	  </varlistentry>

	  <varlistentry>
	    <term><filename>-tdir TESTDIR</></term>
	    <term><filename>-tdir 'TDIR1 TDIR2 [...]'</></term>
	    <listitem>
	      <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
		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
		be used.</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>

	  <varlistentry>
	    <term><filename>-addr EMAIL</></term>
	    <term><filename>-addr 'EMAIL1 EMAIL2 [...]'</></term>
	    <listitem>
	      <para>Send the results (namely, <filename>output.txt</>,
		<filename>genmake_local</>, <filename>genmake_state</>, and
		<filename>Makefile</>) to the specified email addresses.  The
		results are gzipped, placed in a tar file, MIME encoded, and
		sent to the specified address.  If no email addresses are
		specified, no mail is sent.</para>
	    </listitem>
	  </varlistentry>

	  <varlistentry>
	    <term><filename>-mpi</></term>
	    <listitem>
	      <para>If the necessary files
	      (<filename>TESTDIR/code/CPP_EEOPTIONS.h_mpi</> and
	      <filename>TESTDIR/code/SIZE.h_mpi</>) exist, then use them for an
	      MPI--enabled run.  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
	      found in the <ulink
	      url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
	      MITgcm-contrib area</ulink></para>
	    </listitem>
	  </varlistentry>

	  <varlistentry>
	    <term><filename>-command='some command to run'</></term>
	    <listitem>
	      <para>For some tests, particularly MPI runs, the default "make
	      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://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
	      MITgcm-contrib area</ulink></para>
	    </listitem>
	  </varlistentry>

	</variablelist>

	<para>The <filename>testreport</> script will write progress to the
	  screen (stdout) as it runs.  In addition, it will create a
	  <filename>tr_out.txt</> file that contains a brief comparison of the
	  current output with the "known-good" output.</para>

      </sect3>

    </sect2>


    <sect2 id="packages">
      <title>Creating MITgcm Packages</title>

      <para>Optional parts of code have been separated from the MITgcmUV core
	driver code and organised into packages.  The packaging structure
	provides a mechanism for maintaining suites of code, specific to
	particular classes of problems, in a way that is cleanly separated from
	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
	implementing GM/Redi mixing. This code uses the package name</para>

    </sect2>

  </sect1>

  <sect1>
    <title>Chris's Notes...</title>

<programlisting>
           MITgcmUV Packages
           =================

  Optional parts of code are separated from
the MITgcmUV core driver code and organised into
packages. The packaging structure provides a mechanism for
maintaining suites of code, specific to particular
classes of problem, in a way that is cleanly
separated from the generic fluid dynamical engine.

 The MITgcmUV packaging structure is describe
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

Package states
==============

 Packages can be any one of four states, included,
 excluded, enabled, disabled as follows:

 included(excluded) compile time state which
                    includes(excludes) package
                    code and routine calls from
                    compilation/linking etc...

 enabled(disabled)  run-time state which
                    enables(disables) package code
                    execution.

 Every call to a ${pkg}_... routine from outside the package
 should be placed within both a
 #ifdef ALLOW_${PKG} ... block and a
 if ( use${Pkg} ) ... then block.
 Package states are generally not expected to change during
 a model run.

Package structure
=================

o  Each package gets its runtime configuration
   parameters from a file named "data.${pkg}"
   Package runtime config. options are imported
   into a common block held in a header file
   called "${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
   through logical flags use${Pkg}.
   The information is loaded from a
   global package setup file called "data.pkg".
   The use${Pkg} flags are not used within
   individual packages.

o  Included in "${PKG}.h" is a logical flag
   called ${Pkg}IsOn. The "${PKG}.h" header file can be imported
   by other packages to check dependencies and requirements
   from other packages ( see "Package Boot Sequence" section).
   NOTE: This procedure is not presently implemented,
   ----- neither for kpp nor for gmRedi.

CPP Flags
=========

    1. 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.

       Core model code .....

       #include "PACKAGES_CONFIG.h"
       #include "CPP_OPTIONS.h"
         :
         :
         :

       #ifdef ALLOW_${PKG}
         if ( use${Pkg} ) CALL ${PKG}_DO_SOMETHING(...)
       #endif

    2. 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".


Package Boot Sequence
=====================

    Calls to package routines within the core code timestepping
    loop can vary. However, all packages follow a required
    "boot" sequence outlined here:

    1. S/R PACKAGES_BOOT()
            :
        CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... )
 

    2. S/R PACKAGES_READPARMS()
            :
        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_READPARMS( retCode )
        #endif

    3. S/R PACKAGES_INIT_FIXED()
            :
        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_INIT_FIXED( retCode )
        #endif

    4. S/R PACKAGES_CHECK()
            :
        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_CHECK( retCode )
        #else
          if ( use${Pkg} )
     &       CALL PACKAGES_CHECK_ERROR('${PKG}')
        #endif

    5. S/R PACKAGES_INIT_VARIABLES()
            :
        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_INIT_VARIA( )
        #endif

Package Output
==============
     6. S/R DO_THE_MODEL_IO

        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_OUTPUT( )
        #endif

     7. S/R PACKAGES_WRITE_PICKUP()

        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_WRITE_PICKUP( )
        #endif

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 )
          2) for simple pkg setup, this part is done inside ${PKG}_READPARMS

     - ${PKG}_CHECK() 
    is responsible for validating
    basic package setup and inter-package dependencies.
    ${PKG}_CHECK can import other package parameters it may
    need to check. This is done through header files "${PKG}.h".
    It is assumed that parameters owned by other packages
    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}_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) 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.
           2) 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

Summary
=======

- CPP options:
  -----------------------
  * ALLOW_${PKG}         include/exclude package for compilation

- FORTRAN logical:
  -----------------------
  * use${Pkg}            enable package for execution at runtime
                         -> declared in PARAMS.h
  * ${Pkg}IsOn           for package cross-dependency check
                         -> declared in ${PKG}.h
                         N.B.: Not presently used!

- header files
  -----------------------
  * ${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
  -----------------------
  * ${pkg}_readparms.F    reads parameters from file data.${pkg}
  * ${pkg}_init_fixed.F   complete the package setup
  * ${pkg}_check.F        checks package dependencies and consistencies
  * ${pkg}_init_varia.F   initialises package-related fields
  * ${pkg}_... .F         package source code
  * ${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
</programlisting>

  </sect1>


</article>

