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<!DOCTYPE ARTICLE PUBLIC "-//OASIS//DTD DocBook V4.1//EN"> |
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$Header: /u/gcmpack/MITgcm/doc/devel_HOWTO.sgml,v 1.13 2010/05/15 01:44:50 jmc Exp $ |
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<article id="MITgcm-Development-HOWTO"> |
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<articleinfo> |
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<title>MITgcm Development HOWTO</title> |
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<author> |
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<firstname>Ed</firstname> |
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<surname>Hill III</surname> |
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<affiliation> |
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<address><email>eh3@mit.edu</email></address> |
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</affiliation> |
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</author> |
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<revhistory> |
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<revision> |
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<revnumber>0.01</revnumber> |
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<date>2003-08-07</date> |
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<authorinitials>eh3</authorinitials> |
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<revremark> |
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Initial version. |
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</revremark> |
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</revision> |
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<revision> |
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<revnumber>0.02</revnumber> |
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<date>2010-01-21</date> |
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<authorinitials>jmc</authorinitials> |
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<revremark> |
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update links. |
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</revremark> |
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</revision> |
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<revision> |
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<revnumber>0.03</revnumber> |
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<date>2010-04-25</date> |
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<authorinitials>jmc</authorinitials> |
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<revremark> |
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Add subsection "Developer settings" (under CVS Repository). |
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</revremark> |
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</revision> |
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</revhistory> |
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<abstract> |
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<para>This document describes how to develop software for the |
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MITgcm project.</para> |
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</abstract> |
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</articleinfo> |
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<sect1 id="intro"> |
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<title>Introduction</title> <para>The purpose of this document is |
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to help new developers get "up to speed" with MITgcm |
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development.</para> |
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<sect2> |
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<title>New Versions of This Document</title> <para>You can |
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obtain the latest version of this document <ulink |
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url="http://mitgcm.org/public/docs.html">online</ulink> in |
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various formats.</para> |
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</sect2> |
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<sect2> |
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<title>Feedback and corrections</title> <para>If you have |
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questions or comments about this document, please feel free to |
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<ulink url="mailto:MITgcm-support@mitgcm.org">contact the |
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authors</ulink>. |
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</para> |
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</sect2> |
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</sect1> |
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<sect1 id="background"> |
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<title>Background</title> |
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<sect2> |
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<title>User Manual</title> |
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<para>Before jumping into development, please familiarize yourself with |
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the <ulink url="http://mitgcm.org/public/docs.html"> MITgcm user manual |
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</ulink>. This document contains volumes of useful information and is |
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included here by reference.</para> |
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|
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<!-- |
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<para>Also, a "snapshot" or <ulink |
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url="http://mitgcm.org/dev_docs/">development version</ulink> of |
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the user manual may be available, though this is only put on the |
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web for testing purposes.</para> |
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--> |
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</sect2> |
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<sect2> |
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<title>Prerequisites</title> <para>To develop for MITgcm project |
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you will need a UNIX or UNIX-like set of build tools including |
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the following:</para> |
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<blockquote> |
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<simplelist type="inline"> |
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<member>CVS client</member> |
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<member>make or (preferably) GNU make</member> |
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<member>FORTRAN compiler</member> |
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<member>C compiler</member> |
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<member>[ba]sh and [t]csh shells</member> |
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<member>PERL</member> |
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<member>LaTeX and LaTeX2HTML</member> |
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</simplelist> |
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</blockquote> |
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<para>Essentially all of the work described here has been tested |
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on recent versions of Red Hat Linux (eg. 7.3 through 9). Except |
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where noted, all shell commands will be provided using bash |
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syntax. |
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</para> |
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</sect2> |
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</sect1> |
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<sect1 id="cvs"> |
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<title>CVS Repository</title> |
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<sect2> |
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<title>Layout</title> |
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<para>Unlike many open source projects, the MITgcm CVS tree does |
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not follow a simple "src", "docs", "share", and "test" directory |
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layout. Instead, there are multiple higher-level directories |
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that each, to some extent, depend upon the presence of the |
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others. The tree currently resembles:</para> |
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<programlisting>gcmpack/ |
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CVSROOT -hidden- |
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MITgcm code |
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bin empty |
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doc basic developpment documentation |
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eesupp execution environment support code (wrapper) |
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exe empty |
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jobs runtime shell scripts for |
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various platforms (not maintained) |
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lsopt line search |
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model main dynamics (core) |
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optim line search interface |
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pkg alternate and optional numerics, etc. |
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tools scripts to build (and test) |
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utils pre/post processing tools (matlab, ..) |
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verification standard regression tests + examples |
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+ documented examples (tutorials) |
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tutorial_examples (only in release1 branch) |
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|
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MITgcm_contrib contributed code |
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acesgrid.org build acesgrid web site |
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development experimental stuff |
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gfd_lab -?- |
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manual source of MITgcm documentation |
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mitgcm.org build web site |
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old_develop old and early development source |
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misc -?- |
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models -?- |
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packages -?- |
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preprocess -?- |
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pdfs some pdfs |
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planetinabottle.org unfinished web site |
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www.ecco-group.org build ecco web site ? |
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</programlisting> |
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<!-- |
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<para>Efforts are underway to reduce the complexity.</para> |
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--> |
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</sect2> |
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<!-- |
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<sect2> |
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<title>Releases</title> <para>Currently, there are two main |
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branches:</para> |
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<itemizedlist mark="bullet"> |
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<listitem> |
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<para>Development</para> |
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<itemizedlist mark="bullet"> |
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<listitem> |
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<para>MAIN</para> |
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</listitem> |
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<listitem> |
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<para>ecco-branch</para> |
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</listitem> |
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</itemizedlist> |
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</listitem> |
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<listitem> |
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<para>Production</para> |
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<itemizedlist mark="bullet"> |
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<listitem> |
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<para>Release1</para> |
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</listitem> |
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<listitem> |
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<para>Release2</para> |
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</listitem> |
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</itemizedlist> |
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</listitem> |
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</itemizedlist> |
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</sect2> |
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--> |
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<sect2> |
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<title>Branches</title> |
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<para>As shown in the online <ulink |
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url="http://mitgcm.org/viewvc/MITgcm/MITgcm/model/src/forward_step.F?view=graph"> |
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dimitri |
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ViewCVS-generated tree</ulink>, the MITgcm codebase is split into |
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branches or "lines" under which development proceeds. The main line |
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of development is referred to as the "MAIN" version of the code. |
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</para> |
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<para>Periodically, a "Release" branch is formed from the "MAIN" |
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development branch. This is done in order to create a relatively stable |
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reference point for both users and developers. The intent is that once a |
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release branch has been created, only bug-fixes will be added to it. |
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Meanwhile, development (which might "break" or otherwise render invalid |
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the documentation, tutorials, and/or examples contained within a release |
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branch) is allowed to continue along the MAIN line.</para> |
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</sect2> |
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<sect2> |
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<title> Developer settings </title> |
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<para>CVS is a convenient tool to keep up-to-date a personal copy of the |
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MITgcm code (see: <ulink url="http://mitgcm.org/public/using_cvs.html"> |
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using CVS </ulink>). The same tool is used by developers to |
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incorporate any change into the repository. However, this later |
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function requires specific settings, as detailed here after:</para> |
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<orderedlist> |
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<listitem> |
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<para> You will need an account (loggin access) to the server |
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"mitgcm.org" with the proper group setting (e.g., |
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group "gcmctrb" to add/modify code into MITgcm_contrib). |
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This kind of account is granted only upon well motivated request. |
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The access to the server mitgcm.org is through ssh-key authorization |
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which will need to be set properly on both side (on your local machine |
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and on your server account). You need to be able to |
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to ssh to mitgcm.org (or <filename>ssh MY_USER_NAME@mitgcm.org</filename> |
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in case of different user-name on both sides) to proceed further.</para> |
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</listitem> |
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<listitem> |
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<para> You need to register to the |
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<ulink url="http://mitgcm.org/mailman/listinfo/mitgcm-cvs"> |
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mitgcm-cvs </ulink> mailing list. |
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This ensures that other developers will receive email notification |
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when you make changes; you will also receive as well such email |
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when others make changes to the repository. |
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</para> |
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</listitem> |
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<listitem> |
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<para> It is highly recommended that you register also to the |
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<ulink url="http://mitgcm.org/mailman/listinfo/mitgcm-devel"> |
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mitgcm-devel </ulink> mailing list (expect a short delay for |
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this request to be processed). |
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This list is intended for developer discussions. |
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</para> |
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</listitem> |
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<listitem> |
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<para> The standard anonymous mode (using "cvsanon", as mentionned |
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<ulink url="http://mitgcm.org/public/source_code.html"> |
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here </ulink>) does not allow check-in ("cvs commit") permission. |
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Instead, you will need to set our CVS environment as follow:</para> |
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<screen> |
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$ export CVS_RSH=ssh |
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$ export CVSROOT=':ext:MY_USER_NAME@mitgcm.org:/u/gcmpack' |
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</screen> |
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<para> After downloading a directory, e.g.: <filename>myCopy</filename>, |
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from the CVS repository (e.g., |
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<filename>MITgcm_contrib/thisPart</filename>) using the command:</para> |
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<screen> |
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$ cvs co -P -d myCopy MITgcm_contrib/thisPart |
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</screen> |
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<para> the type of CVS environment which has been used |
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is stored in the file <filename>myCopy/CVS/Root</filename> |
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and makes it difficult to re-use, for cvs-commit purpose, |
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a cvs local copy (<filename>myCopy</filename>) which was obtained |
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using the CVS anonymous mode.</para> |
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</listitem> |
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<listitem> |
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<para> At this stage, you should be able to send your modified source |
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file (e.g., <filename>src_file</filename>) from your local copy directory |
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(<filename>myCopy</filename>) to the CVS repository |
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(<filename>MITgcm_contrib/thisPart</filename>) using the command |
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"cvs commit":</para> |
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<screen> |
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$ cd myCopy |
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$ cvs -n update (optional; check if new changes have been made) |
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$ cvs diff src_file (optional; list your changes) |
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$ cvs commit src_file |
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</screen> |
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<para> It is essential that you provide a short description of the |
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changes you made to <filename>src_file</filename> as you check-in |
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this file (the "cvs commit" command automatically opens your standard |
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editor for this purpose).</para> |
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</listitem> |
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</orderedlist> |
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</sect2> |
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<sect2> |
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<title>Main code development</title> |
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jmc |
1.14 |
<para><emphasis>(formerly named "Tagging" ; this section needs an update) |
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</emphasis></para> |
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|
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edhill |
1.7 |
<para>The intent of tagging is to create "known-good" checkpoints that |
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developers can use as references. Traditionally, MITgcm tagging has |
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maintained the following conventions:</para> |
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edhill |
1.1 |
|
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<orderedlist> |
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<listitem> |
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edhill |
1.7 |
<para>Developer checks out code into a local CVS-managed directory, |
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makes various changes/additions, tests these edits, and eventually |
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reaches a point where (s)he is satisfied that the changes form a new |
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"useful" point in the evolution of the code.</para> |
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1.1 |
</listitem> |
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<listitem> |
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<para>The developer then runs the <ulink |
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jmc |
1.10 |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm/verification/testreport"> |
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testreport</ulink> shell script to see if any problems are introduced. |
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edhill |
1.7 |
While not intended to be exhaustive, the test cases within the |
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verification directory do provide some indication whether gross errors |
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have been introduced. |
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edhill |
1.1 |
</para> |
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</listitem> |
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|
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<listitem> |
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<para>Having satisfied him- or herself that the changes are |
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ready to be committed to the CVS repository, the developer |
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then:</para> |
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<orderedlist> |
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<listitem> |
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edhill |
1.7 |
<para>adds a "checkpointXY_pre" comment (where X is a checkpoint |
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number and Y is a letter) to the <ulink |
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jmc |
1.10 |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm/doc/tag-index"> |
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edhill |
1.7 |
tag-index</ulink> file and checks it into the CVS |
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repository</para> |
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edhill |
1.1 |
</listitem> |
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|
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<listitem> |
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edhill |
1.7 |
<para>submits the set of changes to the CVS repository and adds |
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comments to <filename>tag-index</filename> describing what the |
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changes are along with a matching "checkpointXY_post" entry</para> |
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edhill |
1.1 |
</listitem> |
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</orderedlist> |
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</listitem> |
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</orderedlist> |
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|
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edhill |
1.7 |
<para>The result of this tagging procedure is a sequence of development |
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|
|
checkpoints with comments which resembles:</para> |
| 354 |
edhill |
1.1 |
|
| 355 |
|
|
<programlisting> |
| 356 |
|
|
checkpoint50e_post |
| 357 |
|
|
o make KPP work with PTRACERS |
| 358 |
|
|
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
| 359 |
|
|
nearly a copy of kpp_transport_s |
| 360 |
|
|
- there is no analogue to SurfaceTendencyS, so I have to use |
| 361 |
|
|
gPtr(of the surface layer) instead |
| 362 |
|
|
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
| 363 |
|
|
checkpoint50e_pre |
| 364 |
|
|
|
| 365 |
|
|
checkpoint50d_post |
| 366 |
|
|
o change kpp output from multiple-record state files to single-record state |
| 367 |
|
|
files analogous to write_state.F |
| 368 |
|
|
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
| 369 |
|
|
analogous to the cg2d-related output. |
| 370 |
|
|
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
| 371 |
|
|
so that writing to internal file fn (with length 512) fails. |
| 372 |
|
|
checkpoint50d_pre |
| 373 |
|
|
</programlisting> |
| 374 |
|
|
|
| 375 |
edhill |
1.7 |
<para>This information can be used to refer to various stages of the code |
| 376 |
|
|
development. For example, bugs can be traced to individual sets of CVS |
| 377 |
|
|
checkins based upon their first appearance when comparing the results from |
| 378 |
|
|
different checkpoints.</para> |
| 379 |
edhill |
1.1 |
|
| 380 |
|
|
</sect2> |
| 381 |
|
|
</sect1> |
| 382 |
|
|
|
| 383 |
|
|
|
| 384 |
edhill |
1.2 |
<sect1 id="coding"> |
| 385 |
edhill |
1.3 |
<title>Coding for MITgcm</title> |
| 386 |
|
|
|
| 387 |
|
|
<sect2 id="build_tools"> |
| 388 |
|
|
<title>Build Tools</title> |
| 389 |
|
|
|
| 390 |
edhill |
1.4 |
<para>Many Open Source projects use the "GNU Autotools" to help streamline |
| 391 |
|
|
the build process for various Unix and Unix-like architectures. For a |
| 392 |
|
|
user, the result is the common "configure" (that is, |
| 393 |
|
|
"<filename>./configure && make && make install</filename>") commands. |
| 394 |
|
|
For MITgcm, the process is similar. Typical commands are:</para> |
| 395 |
edhill |
1.3 |
|
| 396 |
|
|
<screen> |
| 397 |
jmc |
1.14 |
$ genmake2 -mods=../code |
| 398 |
edhill |
1.5 |
$ make depend |
| 399 |
|
|
$ make |
| 400 |
edhill |
1.3 |
</screen> |
| 401 |
|
|
|
| 402 |
edhill |
1.4 |
<para>The following sections describe the individual steps in the build |
| 403 |
|
|
process.</para> |
| 404 |
|
|
|
| 405 |
edhill |
1.3 |
<sect3 id="genmake"> |
| 406 |
|
|
<title>The <filename>genmake2</> Utility</title> |
| 407 |
|
|
|
| 408 |
jmc |
1.14 |
<para><emphasis>(Note: the older <filename>genmake</> |
| 409 |
|
|
has been replaced by <filename>genmake2</>)</emphasis></para> |
| 410 |
edhill |
1.4 |
|
| 411 |
|
|
<para>The first step in any MITgcm build is to create a Unix-style |
| 412 |
|
|
<filename>Makefile</filename> which will be parsed by |
| 413 |
|
|
<filename>make</filename> to specify how to compile the MITgcm source |
| 414 |
|
|
files. For more detailed descriptions of what the make tools are and |
| 415 |
|
|
how they are used, please see:</para> |
| 416 |
edhill |
1.3 |
|
| 417 |
|
|
<itemizedlist> |
| 418 |
|
|
<listitem> |
| 419 |
edhill |
1.4 |
<para><ulink url="http://www.gnu.org/software/make/make.html"> |
| 420 |
|
|
http://www.gnu.org/software/make/make.html</></para> |
| 421 |
edhill |
1.3 |
</listitem> |
| 422 |
|
|
<listitem> |
| 423 |
edhill |
1.4 |
<para><ulink url="http://www.oreilly.com/catalog/make2/"> |
| 424 |
|
|
http://www.oreilly.com/catalog/make2/</></para> |
| 425 |
edhill |
1.3 |
</listitem> |
| 426 |
|
|
</itemizedlist> |
| 427 |
|
|
|
| 428 |
edhill |
1.4 |
<para>Genmake can often be invoked successfully with a command line as |
| 429 |
|
|
simple as:</para> |
| 430 |
|
|
|
| 431 |
|
|
<screen> |
| 432 |
edhill |
1.5 |
$ genmake2 -mods=../code |
| 433 |
edhill |
1.4 |
</screen> |
| 434 |
|
|
|
| 435 |
|
|
<para>However, some systems (particularly commercial Unixes that lack a |
| 436 |
|
|
more modern "/bin/sh" implementation or that have shells installed in |
| 437 |
|
|
odd locations) may require an explicit shell invocation such as one of |
| 438 |
|
|
the following: </para> |
| 439 |
|
|
|
| 440 |
|
|
<screen> |
| 441 |
edhill |
1.5 |
$ /usr/bin/sh genmake2 -make=gmake -mods=../code |
| 442 |
|
|
$ /opt/gnu/bin/bash genmake2 -ieee -make=/usr/local/bin/gmake -mods=../code |
| 443 |
edhill |
1.4 |
</screen> |
| 444 |
|
|
|
| 445 |
|
|
<para>The genmake2 code has been written in a Bourne and BASH (v1) |
| 446 |
|
|
compatible syntax so it should work with most "sh" and all recent "bash" |
| 447 |
|
|
implementations.</para> |
| 448 |
|
|
|
| 449 |
|
|
<para>As the name implies, <filename>genmake2</filename> generates a |
| 450 |
|
|
<filename>Makefile</filename>. It does so by first parsing the |
| 451 |
|
|
information supplied from the following sources</para> |
| 452 |
edhill |
1.3 |
|
| 453 |
|
|
<orderedlist> |
| 454 |
|
|
<listitem> |
| 455 |
jmc |
1.6 |
<para>a <filename>gemake_local</filename> file in the current |
| 456 |
edhill |
1.4 |
directory</para> |
| 457 |
edhill |
1.3 |
</listitem> |
| 458 |
|
|
<listitem> |
| 459 |
|
|
<para>directly from command-line options</para> |
| 460 |
|
|
</listitem> |
| 461 |
|
|
<listitem> |
| 462 |
edhill |
1.4 |
<para>an "options file" as specified by the command-line option |
| 463 |
|
|
<filename>-optfile='FILENAME'</filename></para> |
| 464 |
edhill |
1.3 |
</listitem> |
| 465 |
jmc |
1.14 |
<listitem> |
| 466 |
|
|
<para> a <filename>packages.conf</filename> file (in the current |
| 467 |
|
|
directory or in one of the "MODS" directories, see below) |
| 468 |
|
|
which contains the specific list of packages to compile |
| 469 |
|
|
</para> |
| 470 |
|
|
</listitem> |
| 471 |
edhill |
1.3 |
</orderedlist> |
| 472 |
|
|
|
| 473 |
edhill |
1.4 |
<para>then checking certain dependency rules (the package dependencies), |
| 474 |
|
|
and finally writing a <filename>Makefile</filename> based upon the |
| 475 |
|
|
source code that it finds. For convenience within various Unix |
| 476 |
|
|
shells, <filename>genmake2</> supports both "long"- and "short"-style |
| 477 |
|
|
options. A complete list of the available options can be obtained |
| 478 |
|
|
from:</para> |
| 479 |
edhill |
1.3 |
|
| 480 |
|
|
<screen> |
| 481 |
edhill |
1.5 |
$ genmake2 -help |
| 482 |
edhill |
1.3 |
</screen> |
| 483 |
|
|
|
| 484 |
edhill |
1.4 |
<para>The most important options for <filename>genmake2</> are:</para> |
| 485 |
edhill |
1.3 |
|
| 486 |
|
|
<variablelist> |
| 487 |
|
|
|
| 488 |
|
|
<varlistentry> |
| 489 |
|
|
<term><filename>--optfile=/PATH/FILENAME</></term> |
| 490 |
edhill |
1.4 |
|
| 491 |
edhill |
1.3 |
<listitem> |
| 492 |
edhill |
1.4 |
<para>This specifies the "options file" that should be used for a |
| 493 |
|
|
particular build. The options file is a convenient and |
| 494 |
|
|
machine-indepenent way of specifying parameters such as the |
| 495 |
|
|
FORTRAN compiler (<filename>FC=</>), FORTRAN compiler |
| 496 |
|
|
optimization flags (<filename>FFLAGS=</>), and the locations of |
| 497 |
|
|
various platform- and/or machine-specific tools |
| 498 |
|
|
(eg. <filename>MAKEDEPEND=</>). As with <filename>genmake2</>, |
| 499 |
|
|
all options files should be written to be compatible with |
| 500 |
|
|
Bourne--shell ("sh" or "BASH v1") syntax. Examples of various |
| 501 |
|
|
options files can be found in |
| 502 |
|
|
<filename>$ROOTDIR/tools/build_options</>.</para> |
| 503 |
|
|
|
| 504 |
|
|
<para>If no "optfile" is specified (either through the command lin |
| 505 |
|
|
or the environment variable), genmake2 will try to make a |
| 506 |
|
|
reasonable guess from the list provided in |
| 507 |
|
|
<filename>$ROOTDIR/tools/build_options</>. The method used for |
| 508 |
|
|
making this guess is to first determine the combination of |
| 509 |
|
|
operating system and hardware (eg. "linux_ia32") and then find a |
| 510 |
|
|
working Fortran compiler within the user's path. When these |
| 511 |
|
|
three items have been identified, genmake2 will try to find an |
| 512 |
|
|
optfile that has a matching name. </para> |
| 513 |
|
|
|
| 514 |
|
|
<para>Everyone is encouraged to submit their options files to the |
| 515 |
|
|
MITgcm project for inclusion (please send to |
| 516 |
|
|
<email>MITgcm-support@mitgcm.org</email>). We are particularly |
| 517 |
|
|
grateful for options files tested on new or unique |
| 518 |
|
|
platforms!</para> |
| 519 |
edhill |
1.3 |
</listitem> |
| 520 |
edhill |
1.4 |
|
| 521 |
edhill |
1.3 |
</varlistentry> |
| 522 |
|
|
|
| 523 |
|
|
<varlistentry> |
| 524 |
edhill |
1.5 |
<term><filename>-adof=/path/to/file</></term> |
| 525 |
|
|
<term><filename>-adoptfile=/path/to/file</></term> |
| 526 |
|
|
<listitem> |
| 527 |
|
|
<para>This option specifies the "adjoint" or automatic |
| 528 |
|
|
differentiation options file to be used. The file is analogous |
| 529 |
|
|
to the "optfile" defined above but it specifies information for |
| 530 |
|
|
the AD build process. The default file is located in <filename> |
| 531 |
|
|
$ROOTDIR/tools/adjoint_options/adjoint_default </> and it |
| 532 |
|
|
defines the "TAF" and "TAMC" compilers. An alternate version is |
| 533 |
|
|
also available at <filename> |
| 534 |
|
|
$ROOTDIR/tools/adjoint_options/adjoint_staf </> that selects the |
| 535 |
|
|
newer "STAF" compiler. As with any compilers, it is helpful to |
| 536 |
|
|
have their directories listed in your $PATH environment |
| 537 |
|
|
variable.</para> |
| 538 |
|
|
</listitem> |
| 539 |
|
|
</varlistentry> |
| 540 |
|
|
|
| 541 |
|
|
<varlistentry> |
| 542 |
edhill |
1.4 |
<term><filename>-mods=DIR</></term> |
| 543 |
|
|
<term><filename>-mods='DIR1 [DIR2 ...]'</></term> |
| 544 |
edhill |
1.3 |
<listitem> |
| 545 |
edhill |
1.4 |
<para>This option specifies a list of directories containing |
| 546 |
|
|
"modifications". These directories contain files with names |
| 547 |
|
|
that may (or may not) exist in the main MITgcm source tree but |
| 548 |
|
|
will be overridden by any identically-named sources within the |
| 549 |
|
|
"MODS" directories. The order of precedence for this |
| 550 |
|
|
"name-hiding" is as follows:</para> |
| 551 |
|
|
<itemizedlist> |
| 552 |
|
|
<listitem><para>"MODS" directories (in the order given) |
| 553 |
|
|
</para></listitem> |
| 554 |
|
|
<listitem><para>Packages either explicitly specified or |
| 555 |
|
|
provided by default (in the order given)</para></listitem> |
| 556 |
|
|
<listitem><para>Packages included due to package dependencies |
| 557 |
|
|
(in the order that that package dependencies are |
| 558 |
|
|
parsed)</para></listitem> |
| 559 |
|
|
<listitem><para>The "standard dirs" (which may have been |
| 560 |
|
|
specified by the "-standarddirs" option)</para></listitem> |
| 561 |
|
|
</itemizedlist> |
| 562 |
jmc |
1.14 |
</listitem> |
| 563 |
|
|
</varlistentry> |
| 564 |
|
|
|
| 565 |
|
|
<varlistentry> |
| 566 |
|
|
<term><filename>-pgroups=/PATH/FILENAME</></term> |
| 567 |
|
|
<listitem> |
| 568 |
|
|
<para>This option specifies the file where package groups are |
| 569 |
|
|
defined. If not set, the package-groups definition will |
| 570 |
|
|
be read from |
| 571 |
|
|
<filename>$ROOTDIR/pkg/pkg_groups</>.</para> |
| 572 |
|
|
<para> |
| 573 |
|
|
It also contains the default list of packages (defined |
| 574 |
|
|
as the group <filename>"default_pkg_list"</>) which is used |
| 575 |
|
|
when no specific package list (file: <filename>packages.conf</>) |
| 576 |
|
|
is found in current directory or in any "MODS" directory. |
| 577 |
|
|
</para> |
| 578 |
|
|
</listitem> |
| 579 |
|
|
</varlistentry> |
| 580 |
edhill |
1.4 |
|
| 581 |
jmc |
1.14 |
<varlistentry> |
| 582 |
|
|
<term><filename>-pdepend=/PATH/FILENAME</></term> |
| 583 |
|
|
|
| 584 |
|
|
<listitem> |
| 585 |
|
|
<para>This specifies the dependency file used for packages. If |
| 586 |
|
|
not specified, the default dependency file is |
| 587 |
|
|
<filename>$ROOTDIR/pkg/pkg_depend</>. The syntax for this file is |
| 588 |
|
|
parsed on a line-by-line basis where each line containes either a |
| 589 |
|
|
comment ("#") or a simple "PKGNAME1 (+|-)PKGNAME2" pairwise rule |
| 590 |
|
|
where the "+" or "-" symbol specifies a "must be used with" or a |
| 591 |
|
|
"must not be used with" relationship, respectively. If no rule is |
| 592 |
|
|
specified, then it is assumed that the two packages are compatible |
| 593 |
|
|
and will function either with or without each other.</para> |
| 594 |
edhill |
1.4 |
</listitem> |
| 595 |
|
|
</varlistentry> |
| 596 |
|
|
|
| 597 |
|
|
<varlistentry> |
| 598 |
|
|
<term><filename>-make=/path/to/gmake</></term> |
| 599 |
|
|
<listitem> |
| 600 |
|
|
<para>Due to the poor handling of soft-links and other bugs common |
| 601 |
|
|
with the <filename>make</> versions provided by commercial Unix |
| 602 |
|
|
vendors, GNU <filename>make</filename> (sometimes called |
| 603 |
|
|
<filename>gmake</filename>) should be preferred. This option |
| 604 |
|
|
provides a means for specifying the make program to be |
| 605 |
|
|
used.</para> |
| 606 |
edhill |
1.3 |
</listitem> |
| 607 |
|
|
</varlistentry> |
| 608 |
|
|
|
| 609 |
|
|
</variablelist> |
| 610 |
|
|
|
| 611 |
edhill |
1.4 |
<para>A successful run of <filename>genmake2</> will produce a |
| 612 |
|
|
<filename>Makefile</>, a <filename>PACKAGES_CONFIG.h</> file, and |
| 613 |
|
|
various convenience files used for the automatic differentiation |
| 614 |
|
|
process.</para> |
| 615 |
|
|
|
| 616 |
|
|
<para>In general, it is best to use <filename>genmake2</> on a "clean" |
| 617 |
|
|
directory that is free of all source (*.[F,f],*.[F,f]90) and header |
| 618 |
|
|
(*.h,*.inc) files. Generally, this can be accomplished in an |
| 619 |
jmc |
1.14 |
"un-clean" directory by running "make Clean" followed by "make |
| 620 |
edhill |
1.4 |
makefile".</para> |
| 621 |
edhill |
1.3 |
|
| 622 |
|
|
</sect3> |
| 623 |
|
|
|
| 624 |
|
|
<sect3 id="makefile_use"> |
| 625 |
edhill |
1.5 |
<title>Using the <filename>Makefile</></title> |
| 626 |
edhill |
1.3 |
|
| 627 |
edhill |
1.5 |
<para>Once a <filename>Makefile</> has been created using |
| 628 |
|
|
<filename>genmake2</>, one can build a "standard" (forward |
| 629 |
|
|
simulator) executable using:</para> |
| 630 |
edhill |
1.3 |
|
| 631 |
|
|
<screen> |
| 632 |
jmc |
1.14 |
$ make Clean |
| 633 |
edhill |
1.5 |
$ make depend |
| 634 |
|
|
$ make |
| 635 |
edhill |
1.3 |
</screen> |
| 636 |
|
|
|
| 637 |
jmc |
1.14 |
<para>The "make Clean" step will remove any stale source files, include |
| 638 |
edhill |
1.4 |
files, and links. It is strongly recommended for "un-clean" |
| 639 |
|
|
directories which may contain the (perhaps partial) results of |
| 640 |
jmc |
1.14 |
previous builds. Such "debris" can interfere with the next stage of |
| 641 |
|
|
the build. |
| 642 |
|
|
A more agressive cleaning option, "make CLEAN", can be used to also |
| 643 |
|
|
remove the executable and output files from a previous run.</para> |
| 644 |
edhill |
1.4 |
|
| 645 |
|
|
<para>The "make depend" step will create a large number of symbolic |
| 646 |
|
|
links from the local directory to the source file locations. It also |
| 647 |
|
|
parses these files and creates an extensive list of dependencies |
| 648 |
|
|
within the <filename>Makefile</> itself. The links that exist at this |
| 649 |
|
|
stage are mostly "large F" files (*.F and *.F90) that need to be |
| 650 |
|
|
processed by a C preprocessor ("CPP"). Since "make depend" edits the |
| 651 |
|
|
<filename>Makefile</>, it is important not to skip this step!</para> |
| 652 |
|
|
|
| 653 |
|
|
<para>The final "make" invokes the C preprocessor to produce the "little |
| 654 |
|
|
f" files (*.f and *.f90) and then compiles them to object code using |
| 655 |
|
|
the specified FORTRAN compiler and options. An intermediate script is |
| 656 |
|
|
often used during this stage to further process (usually, make simple |
| 657 |
|
|
substitutions) custom definitions such as variable types within the |
| 658 |
|
|
source files. This additional stage is necessary in order to overcome |
| 659 |
|
|
some of the inconsistencies in the sizes of objects (bytes) between |
| 660 |
edhill |
1.5 |
different compilers. The result of the build process is an executable |
| 661 |
|
|
with the name <filename>mitgcmuv</>.</para> |
| 662 |
|
|
|
| 663 |
|
|
<para>In addition to the forward simulator described above, the |
| 664 |
|
|
<filename>Makefile</> also has a number of targets that can be used to |
| 665 |
|
|
produce various adjoint and tangent-linear builds for optimization and |
| 666 |
|
|
other parameter-sensitivity problems. The additional targets within |
| 667 |
|
|
the <filename>Makefile</> are:</para> |
| 668 |
|
|
|
| 669 |
|
|
<variablelist> |
| 670 |
|
|
|
| 671 |
|
|
<varlistentry> |
| 672 |
|
|
<term><filename>make adall</></term> |
| 673 |
|
|
<listitem> |
| 674 |
|
|
<para>This target produces an <filename>mitgcmuv_ad</> executable |
| 675 |
|
|
using the <filename>taf</> or <filename>staf</> adjoint |
| 676 |
|
|
compiler. See the <filename>genmake2</> "-adof" option for |
| 677 |
|
|
compiler selection.</para> |
| 678 |
|
|
</listitem> |
| 679 |
|
|
</varlistentry> |
| 680 |
|
|
|
| 681 |
|
|
<varlistentry> |
| 682 |
|
|
<term><filename>make ftlall</></term> |
| 683 |
|
|
<listitem> |
| 684 |
|
|
<para>Similar to <filename>make adall</> above, this |
| 685 |
|
|
produces...</para> |
| 686 |
|
|
</listitem> |
| 687 |
|
|
</varlistentry> |
| 688 |
|
|
|
| 689 |
|
|
</variablelist> |
| 690 |
edhill |
1.3 |
|
| 691 |
edhill |
1.5 |
<para>Please report any compilation failures or other build problems to |
| 692 |
|
|
the <email>MITgcm-support@mitgcm.org</email> list.</para> |
| 693 |
edhill |
1.3 |
|
| 694 |
|
|
</sect3> |
| 695 |
|
|
|
| 696 |
|
|
</sect2> |
| 697 |
|
|
|
| 698 |
|
|
<sect2 id="verification"> |
| 699 |
|
|
<title>The Verification Suite</title> |
| 700 |
|
|
|
| 701 |
edhill |
1.4 |
<para>The MITgcm CVS tree (within the <filename>$ROOTDIR/verification/</> |
| 702 |
|
|
directory) includes more than a dozen examples intended for regression |
| 703 |
|
|
testing. Each one of these example directories contains "known-good" |
| 704 |
|
|
output files along with all the input (including both code and data |
| 705 |
|
|
files) required for their re-calculation. These example directories are |
| 706 |
|
|
further broken down into sets of subdirectories |
| 707 |
|
|
(eg. <filename>/input</>, <filename>/code</>) intended to expedite the |
| 708 |
|
|
testing process.</para> |
| 709 |
edhill |
1.3 |
|
| 710 |
|
|
<sect3 id="testreport"> |
| 711 |
|
|
<title>The <filename>testreport</> Utility</title> |
| 712 |
|
|
|
| 713 |
edhill |
1.4 |
<para>Also included in <filename>$ROOTDIR/verification/</> are shell |
| 714 |
|
|
scripts for automated testing. The newest script (which was written |
| 715 |
|
|
to work with <filename>genmake2</>) is called <filename>testreport</>. |
| 716 |
|
|
This script can be used to build different versions of the MITgcm |
| 717 |
|
|
code, run the various examples, compare the output, and (if specified) |
| 718 |
|
|
email the results of each one of these tests to a central |
| 719 |
|
|
repository.</para> |
| 720 |
|
|
|
| 721 |
|
|
<para>On some systems, the testreport script can be run with a command |
| 722 |
|
|
line as simple as:</para> |
| 723 |
|
|
|
| 724 |
|
|
<screen> |
| 725 |
edhill |
1.5 |
$ cd verification |
| 726 |
|
|
$ ./testreport -ieee |
| 727 |
edhill |
1.4 |
</screen> |
| 728 |
|
|
|
| 729 |
|
|
<para>However, some systems (those lacking or wiht a broken "/bin/sh") |
| 730 |
|
|
may require an explicit shell invocation such as:</para> |
| 731 |
|
|
|
| 732 |
|
|
<screen> |
| 733 |
edhill |
1.5 |
$ sh ./testreport -ieee -t 'exp0 exp4' |
| 734 |
|
|
$ /some/path/to/bash ./testreport -ieee -t 'ideal_2D_oce lab_sea natl_box' |
| 735 |
edhill |
1.4 |
</screen> |
| 736 |
edhill |
1.3 |
|
| 737 |
|
|
<para>The <filename>testreport</> script accepts a number of |
| 738 |
edhill |
1.4 |
command-line options which can be listed using the <filename>-help</> |
| 739 |
|
|
option. The most important ones are:</para> |
| 740 |
edhill |
1.3 |
|
| 741 |
|
|
<variablelist> |
| 742 |
|
|
|
| 743 |
|
|
<varlistentry> |
| 744 |
edhill |
1.4 |
<term><filename>-ieee</></term> |
| 745 |
|
|
<listitem> |
| 746 |
|
|
<para>If allowed by the compiler (as defined in the "optfile"), |
| 747 |
|
|
use IEEE arithmetic. This option, along with the GCC compiler, |
| 748 |
|
|
is how the standard results were produced.</para> |
| 749 |
|
|
</listitem> |
| 750 |
|
|
</varlistentry> |
| 751 |
|
|
|
| 752 |
|
|
<varlistentry> |
| 753 |
edhill |
1.3 |
<term><filename>-tdir TESTDIR</></term> |
| 754 |
|
|
<term><filename>-tdir 'TDIR1 TDIR2 [...]'</></term> |
| 755 |
|
|
<listitem> |
| 756 |
edhill |
1.4 |
<para>This option specifies the test directory or list of test |
| 757 |
|
|
directories that should be used. Each of these entries should |
| 758 |
|
|
exactly (note: they are case sensitive!) match the names of |
| 759 |
|
|
directries in <filename>$ROOTDIR/verification/</>. If this |
| 760 |
|
|
option is omitted, then all directories that are properly |
| 761 |
|
|
formatted (that is, containing an <filename>input</> |
| 762 |
|
|
sub-directory and a <filename>results/output.txt</> file) will |
| 763 |
|
|
be used.</para> |
| 764 |
edhill |
1.3 |
</listitem> |
| 765 |
|
|
</varlistentry> |
| 766 |
|
|
|
| 767 |
|
|
<varlistentry> |
| 768 |
|
|
<term><filename>-optfile=/PATH/FILENAME</></term> |
| 769 |
|
|
<term><filename>-optfile '/PATH/F1 [/PATH/F2 ...]'</></term> |
| 770 |
|
|
<listitem> |
| 771 |
edhill |
1.4 |
<para>This specifies a list of "options files" that will be passed |
| 772 |
|
|
to <filename>genmake2</>. If multiple options files are used |
| 773 |
|
|
(say, to test different compilers or different sets of options |
| 774 |
|
|
for the same compiler), then each options file will be used with |
| 775 |
|
|
each of the test directories.</para> |
| 776 |
edhill |
1.3 |
</listitem> |
| 777 |
|
|
</varlistentry> |
| 778 |
|
|
|
| 779 |
|
|
<varlistentry> |
| 780 |
|
|
<term><filename>-addr EMAIL</></term> |
| 781 |
|
|
<term><filename>-addr 'EMAIL1 EMAIL2 [...]'</></term> |
| 782 |
|
|
<listitem> |
| 783 |
|
|
<para>Send the results (namely, <filename>output.txt</>, |
| 784 |
edhill |
1.4 |
<filename>genmake_local</>, <filename>genmake_state</>, and |
| 785 |
|
|
<filename>Makefile</>) to the specified email addresses. The |
| 786 |
|
|
results are gzipped, placed in a tar file, MIME encoded, and |
| 787 |
|
|
sent to the specified address. If no email addresses are |
| 788 |
|
|
specified, no mail is sent.</para> |
| 789 |
|
|
</listitem> |
| 790 |
|
|
</varlistentry> |
| 791 |
|
|
|
| 792 |
|
|
<varlistentry> |
| 793 |
|
|
<term><filename>-mpi</></term> |
| 794 |
|
|
<listitem> |
| 795 |
|
|
<para>If the necessary files |
| 796 |
|
|
(<filename>TESTDIR/code/CPP_EEOPTIONS.h_mpi</> and |
| 797 |
|
|
<filename>TESTDIR/code/SIZE.h_mpi</>) exist, then use them for an |
| 798 |
|
|
MPI--enabled run. Note that the use of MPI typically requires a |
| 799 |
|
|
special command option (see "-command" below) to invoke the MPI |
| 800 |
|
|
executable. Examples of PBS scripts using MPI with testreport can be |
| 801 |
|
|
found in the <ulink |
| 802 |
jmc |
1.10 |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/"> |
| 803 |
edhill |
1.4 |
MITgcm-contrib area</ulink></para> |
| 804 |
|
|
</listitem> |
| 805 |
|
|
</varlistentry> |
| 806 |
|
|
|
| 807 |
|
|
<varlistentry> |
| 808 |
|
|
<term><filename>-command='some command to run'</></term> |
| 809 |
|
|
<listitem> |
| 810 |
|
|
<para>For some tests, particularly MPI runs, the default "make |
| 811 |
|
|
output.txt" is not sufficient. This option allows a more general |
| 812 |
|
|
command (or shell script) to be invoked. Examples of PBS scripts |
| 813 |
|
|
using MPI with testreport can be found in the <ulink |
| 814 |
jmc |
1.10 |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/"> |
| 815 |
edhill |
1.4 |
MITgcm-contrib area</ulink></para> |
| 816 |
edhill |
1.3 |
</listitem> |
| 817 |
|
|
</varlistentry> |
| 818 |
|
|
|
| 819 |
|
|
</variablelist> |
| 820 |
|
|
|
| 821 |
edhill |
1.4 |
<para>The <filename>testreport</> script will write progress to the |
| 822 |
|
|
screen (stdout) as it runs. In addition, it will create a |
| 823 |
|
|
<filename>tr_out.txt</> file that contains a brief comparison of the |
| 824 |
|
|
current output with the "known-good" output.</para> |
| 825 |
edhill |
1.3 |
|
| 826 |
|
|
</sect3> |
| 827 |
|
|
|
| 828 |
|
|
</sect2> |
| 829 |
edhill |
1.2 |
|
| 830 |
edhill |
1.4 |
|
| 831 |
edhill |
1.2 |
<sect2 id="packages"> |
| 832 |
edhill |
1.3 |
<title>Creating MITgcm Packages</title> |
| 833 |
edhill |
1.2 |
|
| 834 |
edhill |
1.4 |
<para>Optional parts of code have been separated from the MITgcmUV core |
| 835 |
|
|
driver code and organised into packages. The packaging structure |
| 836 |
|
|
provides a mechanism for maintaining suites of code, specific to |
| 837 |
|
|
particular classes of problems, in a way that is cleanly separated from |
| 838 |
|
|
the generic fluid dynamical engine.</para> |
| 839 |
|
|
|
| 840 |
|
|
<para>The MITgcmUV packaging structure is described below using generic |
| 841 |
jmc |
1.11 |
package names ${pkg}. A concrete examples of a package is the code for |
| 842 |
edhill |
1.4 |
implementing GM/Redi mixing. This code uses the package name</para> |
| 843 |
edhill |
1.2 |
|
| 844 |
|
|
</sect2> |
| 845 |
|
|
|
| 846 |
|
|
</sect1> |
| 847 |
|
|
|
| 848 |
|
|
<sect1> |
| 849 |
|
|
<title>Chris's Notes...</title> |
| 850 |
|
|
|
| 851 |
|
|
<programlisting> |
| 852 |
|
|
MITgcmUV Packages |
| 853 |
|
|
================= |
| 854 |
|
|
|
| 855 |
|
|
Optional parts of code are separated from |
| 856 |
|
|
the MITgcmUV core driver code and organised into |
| 857 |
|
|
packages. The packaging structure provides a mechanism for |
| 858 |
|
|
maintaining suites of code, specific to particular |
| 859 |
|
|
classes of problem, in a way that is cleanly |
| 860 |
|
|
separated from the generic fluid dynamical engine. |
| 861 |
|
|
|
| 862 |
|
|
The MITgcmUV packaging structure is describe |
| 863 |
|
|
below using generic package names ${pkg}. |
| 864 |
|
|
A concrete examples of a package is the code |
| 865 |
|
|
for implementing GM/Redi mixing. This code uses |
| 866 |
|
|
the package name |
| 867 |
|
|
* ${PKG} = GMREDI |
| 868 |
|
|
* ${pkg} = gmredi |
| 869 |
|
|
* ${Pkg} = gmRedi |
| 870 |
|
|
|
| 871 |
|
|
Package states |
| 872 |
|
|
============== |
| 873 |
|
|
|
| 874 |
|
|
Packages can be any one of four states, included, |
| 875 |
|
|
excluded, enabled, disabled as follows: |
| 876 |
|
|
|
| 877 |
|
|
included(excluded) compile time state which |
| 878 |
|
|
includes(excludes) package |
| 879 |
|
|
code and routine calls from |
| 880 |
|
|
compilation/linking etc... |
| 881 |
|
|
|
| 882 |
|
|
enabled(disabled) run-time state which |
| 883 |
|
|
enables(disables) package code |
| 884 |
|
|
execution. |
| 885 |
|
|
|
| 886 |
|
|
Every call to a ${pkg}_... routine from outside the package |
| 887 |
|
|
should be placed within both a |
| 888 |
|
|
#ifdef ALLOW_${PKG} ... block and a |
| 889 |
|
|
if ( use${Pkg} ) ... then block. |
| 890 |
|
|
Package states are generally not expected to change during |
| 891 |
|
|
a model run. |
| 892 |
|
|
|
| 893 |
|
|
Package structure |
| 894 |
|
|
================= |
| 895 |
|
|
|
| 896 |
|
|
o Each package gets its runtime configuration |
| 897 |
|
|
parameters from a file named "data.${pkg}" |
| 898 |
|
|
Package runtime config. options are imported |
| 899 |
|
|
into a common block held in a header file |
| 900 |
|
|
called "${PKG}.h". |
| 901 |
jmc |
1.8 |
Note: In some packages, the header file "${PKG}.h" is splitted |
| 902 |
|
|
into "${PKG}_PARAMS.h" that contains the package parameters and |
| 903 |
|
|
${PKG}_VARS.h" for the field arrays. |
| 904 |
edhill |
1.2 |
|
| 905 |
|
|
o The core driver part of the model can check |
| 906 |
|
|
for runtime enabling or disabling of individual packages |
| 907 |
|
|
through logical flags use${Pkg}. |
| 908 |
|
|
The information is loaded from a |
| 909 |
|
|
global package setup file called "data.pkg". |
| 910 |
|
|
The use${Pkg} flags are not used within |
| 911 |
|
|
individual packages. |
| 912 |
|
|
|
| 913 |
|
|
o Included in "${PKG}.h" is a logical flag |
| 914 |
|
|
called ${Pkg}IsOn. The "${PKG}.h" header file can be imported |
| 915 |
|
|
by other packages to check dependencies and requirements |
| 916 |
|
|
from other packages ( see "Package Boot Sequence" section). |
| 917 |
|
|
NOTE: This procedure is not presently implemented, |
| 918 |
|
|
----- neither for kpp nor for gmRedi. |
| 919 |
|
|
|
| 920 |
|
|
CPP Flags |
| 921 |
|
|
========= |
| 922 |
|
|
|
| 923 |
|
|
1. Within the core driver code flags of the form |
| 924 |
|
|
ALLOW_${PKG} are used to include or exclude |
| 925 |
|
|
whole packages. The ALLOW_${PKG} flags are included |
| 926 |
jmc |
1.8 |
from a PACKAGES_CONFIG.h file that is automatically |
| 927 |
|
|
generated by genmake2 (see genmake2 section). |
| 928 |
edhill |
1.2 |
held in-line in the CPP_OPTIONS.h header file. |
| 929 |
|
|
e.g. |
| 930 |
|
|
|
| 931 |
|
|
Core model code ..... |
| 932 |
|
|
|
| 933 |
jmc |
1.8 |
#include "PACKAGES_CONFIG.h" |
| 934 |
edhill |
1.2 |
#include "CPP_OPTIONS.h" |
| 935 |
|
|
: |
| 936 |
|
|
: |
| 937 |
|
|
: |
| 938 |
|
|
|
| 939 |
|
|
#ifdef ALLOW_${PKG} |
| 940 |
|
|
if ( use${Pkg} ) CALL ${PKG}_DO_SOMETHING(...) |
| 941 |
|
|
#endif |
| 942 |
|
|
|
| 943 |
|
|
2. Within an individual package a header file, |
| 944 |
|
|
"${PKG}_OPTIONS.h", is used to set CPP flags |
| 945 |
jmc |
1.8 |
specific to that package. It also includes |
| 946 |
|
|
"PACKAGES_CONFIG.h" and "CPP_OPTIONS.h". |
| 947 |
edhill |
1.2 |
|
| 948 |
|
|
|
| 949 |
|
|
Package Boot Sequence |
| 950 |
|
|
===================== |
| 951 |
|
|
|
| 952 |
|
|
Calls to package routines within the core code timestepping |
| 953 |
|
|
loop can vary. However, all packages follow a required |
| 954 |
|
|
"boot" sequence outlined here: |
| 955 |
|
|
|
| 956 |
|
|
1. S/R PACKAGES_BOOT() |
| 957 |
|
|
: |
| 958 |
|
|
CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... ) |
| 959 |
|
|
|
| 960 |
|
|
|
| 961 |
|
|
2. S/R PACKAGES_READPARMS() |
| 962 |
|
|
: |
| 963 |
|
|
#ifdef ALLOW_${PKG} |
| 964 |
|
|
if ( use${Pkg} ) |
| 965 |
|
|
& CALL ${PKG}_READPARMS( retCode ) |
| 966 |
|
|
#endif |
| 967 |
|
|
|
| 968 |
jmc |
1.6 |
3. S/R PACKAGES_INIT_FIXED() |
| 969 |
|
|
: |
| 970 |
|
|
#ifdef ALLOW_${PKG} |
| 971 |
|
|
if ( use${Pkg} ) |
| 972 |
|
|
& CALL ${PKG}_INIT_FIXED( retCode ) |
| 973 |
|
|
#endif |
| 974 |
|
|
|
| 975 |
|
|
4. S/R PACKAGES_CHECK() |
| 976 |
edhill |
1.2 |
: |
| 977 |
|
|
#ifdef ALLOW_${PKG} |
| 978 |
|
|
if ( use${Pkg} ) |
| 979 |
|
|
& CALL ${PKG}_CHECK( retCode ) |
| 980 |
|
|
#else |
| 981 |
|
|
if ( use${Pkg} ) |
| 982 |
|
|
& CALL PACKAGES_CHECK_ERROR('${PKG}') |
| 983 |
|
|
#endif |
| 984 |
|
|
|
| 985 |
jmc |
1.6 |
5. S/R PACKAGES_INIT_VARIABLES() |
| 986 |
edhill |
1.2 |
: |
| 987 |
|
|
#ifdef ALLOW_${PKG} |
| 988 |
|
|
if ( use${Pkg} ) |
| 989 |
jmc |
1.6 |
& CALL ${PKG}_INIT_VARIA( ) |
| 990 |
|
|
#endif |
| 991 |
|
|
|
| 992 |
|
|
Package Output |
| 993 |
|
|
============== |
| 994 |
|
|
6. S/R DO_THE_MODEL_IO |
| 995 |
|
|
|
| 996 |
|
|
#ifdef ALLOW_${PKG} |
| 997 |
|
|
if ( use${Pkg} ) |
| 998 |
jmc |
1.9 |
& CALL ${PKG}_OUTPUT( ) |
| 999 |
edhill |
1.2 |
#endif |
| 1000 |
|
|
|
| 1001 |
jmc |
1.6 |
7. S/R PACKAGES_WRITE_PICKUP() |
| 1002 |
|
|
|
| 1003 |
|
|
#ifdef ALLOW_${PKG} |
| 1004 |
|
|
if ( use${Pkg} ) |
| 1005 |
|
|
& CALL ${PKG}_WRITE_PICKUP( ) |
| 1006 |
|
|
#endif |
| 1007 |
edhill |
1.2 |
|
| 1008 |
|
|
Description |
| 1009 |
|
|
=========== |
| 1010 |
|
|
|
| 1011 |
|
|
- ${PKG}_READPARMS() |
| 1012 |
|
|
is responsible for reading |
| 1013 |
|
|
in the package parameters file data.${pkg}, and storing |
| 1014 |
jmc |
1.8 |
the package parameters in "${PKG}.h" (or in "${PKG}_PARAMS.h"). |
| 1015 |
jmc |
1.6 |
-> called from INITIALISE_FIXED in PACKAGES_READPARMS |
| 1016 |
|
|
|
| 1017 |
|
|
- ${PKG}_INIT_FIXED() |
| 1018 |
|
|
is responsible for completing the internal setup of a package. |
| 1019 |
|
|
-> called from INITIALISE_FIXED in PACKAGES_INIT_FIXED |
| 1020 |
|
|
note: 1) some pkg use instead: |
| 1021 |
|
|
CALL ${PKG}_INITIALISE ( or the old form CALL ${PKG}_INIT ) |
| 1022 |
|
|
2) for simple pkg setup, this part is done inside ${PKG}_READPARMS |
| 1023 |
edhill |
1.2 |
|
| 1024 |
|
|
- ${PKG}_CHECK() |
| 1025 |
|
|
is responsible for validating |
| 1026 |
|
|
basic package setup and inter-package dependencies. |
| 1027 |
|
|
${PKG}_CHECK can import other package parameters it may |
| 1028 |
|
|
need to check. This is done through header files "${PKG}.h". |
| 1029 |
|
|
It is assumed that parameters owned by other packages |
| 1030 |
|
|
will not be reset during ${PKG}_CHECK(). |
| 1031 |
jmc |
1.6 |
-> called from INITIALISE_FIXED in PACKAGES_CHECK |
| 1032 |
edhill |
1.2 |
|
| 1033 |
jmc |
1.6 |
- ${PKG}_INIT_VARIA() |
| 1034 |
|
|
is responsible for fill-in all package variables with an initial value. |
| 1035 |
|
|
Contains eventually a call to ${PKG}_READ_PICKUP that will read |
| 1036 |
|
|
from a pickup file the package variables required to restart the model. |
| 1037 |
|
|
This routine is called after the core model state has been completely |
| 1038 |
|
|
initialised but before the core model timestepping starts. |
| 1039 |
|
|
-> called from INITIALISE_VARIA in PACKAGES_INIT_VARIABLES |
| 1040 |
|
|
note: the name ${PKG}_INIT_VARIA is not yet standard and some pkg |
| 1041 |
|
|
use for e.g. ${PKG}_INI_VARS, ${PKG}_INIT_VARIABLES, or the old |
| 1042 |
|
|
form ${PKG}_INIT |
| 1043 |
|
|
|
| 1044 |
jmc |
1.9 |
- ${PKG}_OUTPUT( ) |
| 1045 |
jmc |
1.8 |
is responsible for writing time-average fields to output files |
| 1046 |
|
|
(but the cumulating step is done within the package main S/R). |
| 1047 |
jmc |
1.6 |
Can also contain other diagnostics (.e.g. CALL ${PKG}_MONITOR) |
| 1048 |
|
|
and write snap-shot fields that are hold in common blocks. Other |
| 1049 |
|
|
temporary fields are directly dump to file where they are available. |
| 1050 |
jmc |
1.9 |
NOTE: 1) the S/R old name ${PKG}_DIAGS is used in some packages |
| 1051 |
|
|
but is beeing replaced by ${PKG}_OUTPUT |
| 1052 |
jmc |
1.8 |
to avoid confusion with pkg/diagnostics functionality. |
| 1053 |
|
|
2) the output part is not yet in a standard form and might still |
| 1054 |
|
|
evolve a lot. |
| 1055 |
jmc |
1.6 |
-> called within DO_THE_MODEL_IO |
| 1056 |
|
|
|
| 1057 |
|
|
- ${PKG}_WRITE_PICKUP() |
| 1058 |
|
|
is responsible for writing a package pickup file when necessary for |
| 1059 |
|
|
a restart. (found also the old name: ${PKG}_WRITE_CHECKPOINT ) |
| 1060 |
|
|
-> called from FORWARD_STEP and THE_MODEL_MAIN in PACKAGES_WRITE_PICKUP |
| 1061 |
edhill |
1.2 |
|
| 1062 |
|
|
Summary |
| 1063 |
|
|
======= |
| 1064 |
|
|
|
| 1065 |
|
|
- CPP options: |
| 1066 |
|
|
----------------------- |
| 1067 |
|
|
* ALLOW_${PKG} include/exclude package for compilation |
| 1068 |
|
|
|
| 1069 |
|
|
- FORTRAN logical: |
| 1070 |
|
|
----------------------- |
| 1071 |
|
|
* use${Pkg} enable package for execution at runtime |
| 1072 |
|
|
-> declared in PARAMS.h |
| 1073 |
|
|
* ${Pkg}IsOn for package cross-dependency check |
| 1074 |
|
|
-> declared in ${PKG}.h |
| 1075 |
|
|
N.B.: Not presently used! |
| 1076 |
|
|
|
| 1077 |
|
|
- header files |
| 1078 |
|
|
----------------------- |
| 1079 |
|
|
* ${PKG}_OPTIONS.h has further package-specific CPP options |
| 1080 |
|
|
* ${PKG}.h package-specific common block variables, fields |
| 1081 |
jmc |
1.8 |
or ${PKG}_PARAMS.h package-specific common block parameters |
| 1082 |
|
|
and ${PKG}_VARS.h package-specific common block fields |
| 1083 |
edhill |
1.2 |
|
| 1084 |
|
|
- FORTRAN source files |
| 1085 |
|
|
----------------------- |
| 1086 |
jmc |
1.6 |
* ${pkg}_readparms.F reads parameters from file data.${pkg} |
| 1087 |
|
|
* ${pkg}_init_fixed.F complete the package setup |
| 1088 |
|
|
* ${pkg}_check.F checks package dependencies and consistencies |
| 1089 |
|
|
* ${pkg}_init_varia.F initialises package-related fields |
| 1090 |
|
|
* ${pkg}_... .F package source code |
| 1091 |
jmc |
1.9 |
* ${pkg}_output.F write output to file. |
| 1092 |
jmc |
1.6 |
* ${pkg}_write_pickup.F write a package pickup file to restart the model |
| 1093 |
edhill |
1.2 |
|
| 1094 |
jmc |
1.8 |
New: Subroutine in one package (pkgA) that only contains code which |
| 1095 |
|
|
is connected to a 2nd package (pkgB) (e.g.: gmredi_diagnostics_init.F) |
| 1096 |
|
|
will be named: pkgA_pkgB_something.F |
| 1097 |
|
|
|
| 1098 |
edhill |
1.2 |
- parameter file |
| 1099 |
|
|
----------------------- |
| 1100 |
|
|
* data.${pkg} parameter file |
| 1101 |
|
|
</programlisting> |
| 1102 |
|
|
|
| 1103 |
|
|
</sect1> |
| 1104 |
edhill |
1.1 |
|
| 1105 |
|
|
|
| 1106 |
jmc |
1.11 |
<sect1 id="documentation"> |
| 1107 |
|
|
<title>Editing the Documentation</title> |
| 1108 |
|
|
|
| 1109 |
|
|
<sect2 id="documentation_getting"> |
| 1110 |
|
|
<title>Getting the Docs and Code</title> |
| 1111 |
|
|
|
| 1112 |
|
|
<para>The first step towards editing the documentation is to checkout a |
| 1113 |
|
|
copy of code, docs, and build scripts from the CVS server using:</para> |
| 1114 |
|
|
|
| 1115 |
|
|
<screen> |
| 1116 |
|
|
$ export CVS_RSH=ssh |
| 1117 |
|
|
$ export CVSROOT=':ext:NAME@mitgcm.org:/u/gcmpack' |
| 1118 |
|
|
$ mkdir scratch |
| 1119 |
|
|
$ cvs co -P MITgcm manual mitgcm.org |
| 1120 |
|
|
</screen> |
| 1121 |
|
|
|
| 1122 |
|
|
<para>These commands extract the necessary information from the CVS server |
| 1123 |
|
|
and create a temporary (called <filename>scratch</filename>) directory for |
| 1124 |
|
|
the storage of the HTML and other files that will be created. Please note |
| 1125 |
|
|
that you must either create <filename>scratch</filename> as shown or edit |
| 1126 |
|
|
the various <filename>Makefile</filename>s and scripts used to create the |
| 1127 |
|
|
documentation.</para> |
| 1128 |
|
|
</sect2> |
| 1129 |
|
|
|
| 1130 |
|
|
<sect2> |
| 1131 |
|
|
<title>Editing the Documentation</title> |
| 1132 |
|
|
|
| 1133 |
|
|
<para>The documentation is contained in the <filename>manual</filename> |
| 1134 |
|
|
directory in a raw LaTeX format. The main document is |
| 1135 |
|
|
<filename>manual.tex</filename> and it uses <command>\input{}</command>s |
| 1136 |
|
|
to include the chapters and subsections.</para> |
| 1137 |
|
|
|
| 1138 |
|
|
<para>Since the same LaTeX source is used to produce PostScript, PDF, and |
| 1139 |
|
|
HTML output, care should be taken to follow certain conventions. Two of |
| 1140 |
|
|
the most important are the usage of the <command>\filelink{}{}</command> |
| 1141 |
|
|
and <command>\varlink{}{}</command> commands. Both of these commands have |
| 1142 |
|
|
been defined to simplify the connection between the automatically |
| 1143 |
|
|
generated ("code browser") HTML and the HTML version of the manual |
| 1144 |
|
|
produced by LaTeX2HTML. They each take two arguments (corresponding to |
| 1145 |
|
|
the contents of the two sets of curly braces) which are the text that the |
| 1146 |
|
|
author wishes to be "wrapped" within the link, and a specially formatted |
| 1147 |
|
|
link thats relative to the <filename>MITgcm</filename> directory within |
| 1148 |
|
|
the CVS tree.</para> |
| 1149 |
|
|
|
| 1150 |
|
|
<para>The result is a command that resembles either</para> |
| 1151 |
|
|
|
| 1152 |
|
|
<orderedlist> |
| 1153 |
|
|
<listitem> |
| 1154 |
|
|
<para>a reference to a variable or subroutine name such as |
| 1155 |
|
|
<command>\varlink{tRef}{tRef}</command>, or </para> |
| 1156 |
|
|
</listitem> |
| 1157 |
|
|
|
| 1158 |
|
|
<listitem> |
| 1159 |
|
|
<para>a reference to a file such as |
| 1160 |
|
|
<command>\varlink{tRef}{path-to-the-file_name.F}</command> |
| 1161 |
|
|
where the absolute path to the file is of the form |
| 1162 |
|
|
<filename>/foo/MITgcm/path/to/the/file_name.F</filename></para> |
| 1163 |
|
|
<para>(please note how the leading "/foo/MITgcm" |
| 1164 |
|
|
component of the path is dropped leaving the path |
| 1165 |
|
|
<emphasis>relative</emphasis> to the head of the code |
| 1166 |
|
|
directory and each directory separator "/" is turned |
| 1167 |
|
|
into a "-")</para> |
| 1168 |
|
|
</listitem> |
| 1169 |
|
|
</orderedlist> |
| 1170 |
|
|
|
| 1171 |
|
|
|
| 1172 |
|
|
|
| 1173 |
|
|
</sect2> |
| 1174 |
|
|
|
| 1175 |
|
|
<sect2> |
| 1176 |
|
|
<title>Building the Documentation</title> |
| 1177 |
|
|
|
| 1178 |
|
|
<para>Given the directory structure of <xref |
| 1179 |
|
|
linkend="documentation_getting">, the entire documentation for the web |
| 1180 |
|
|
site can be built using:</para> |
| 1181 |
|
|
|
| 1182 |
|
|
<screen> |
| 1183 |
|
|
$ cd mitgcm.org/devel/buildweb |
| 1184 |
|
|
$ make All |
| 1185 |
|
|
</screen> |
| 1186 |
|
|
|
| 1187 |
|
|
<para>Which builds the PDF from the LaTeX source, creates the HTML output |
| 1188 |
|
|
from the LaTeX source, parses the FORTRAN code base to produce a |
| 1189 |
|
|
hyperlinked HTML version of the source, and then determines the |
| 1190 |
|
|
cross-linking between the various HTML components.</para> |
| 1191 |
|
|
|
| 1192 |
|
|
<para>If there are no errors, the result of the build process (which can |
| 1193 |
|
|
take 30+ minutes on a P4/2.5Ghz) will be contained within a single |
| 1194 |
|
|
directory called <filename>scratch/dev_docs</filename>. This is a freshly |
| 1195 |
|
|
built version of the entire on-line users manual. If you have the correct |
| 1196 |
|
|
permissions, it can be directly copied to the web server area:</para> |
| 1197 |
|
|
|
| 1198 |
|
|
<screen> |
| 1199 |
|
|
$ mv scratch/dev_docs /u/u0/httpd/html |
| 1200 |
|
|
</screen> |
| 1201 |
|
|
|
| 1202 |
|
|
<para>and the update is complete.</para> |
| 1203 |
|
|
|
| 1204 |
|
|
</sect2> |
| 1205 |
|
|
|
| 1206 |
|
|
</sect1> |
| 1207 |
|
|
|
| 1208 |
edhill |
1.1 |
</article> |
| 1209 |
|
|
|
| 1210 |
|
|
|
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