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<!DOCTYPE ARTICLE PUBLIC "-//OASIS//DTD DocBook V4.1//EN"> |
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|
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<article id="MITgcm-Development-HOWTO"> |
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|
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<articleinfo> |
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<title>MITgcm Development HOWTO</title> |
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|
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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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|
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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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|
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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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|
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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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|
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<sect1 id="background"> |
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<title>Background</title> |
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|
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<sect2> |
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<title>User Manual</title> |
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|
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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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|
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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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|
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</sect1> |
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|
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<sect1 id="cvs"> |
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<title>CVS Repository</title> |
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|
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<sect2> |
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<title>Layout</title> |
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|
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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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|
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<programlisting>gcmpack/ |
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CS-regrid goes into utils |
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CVSROOT -hidden- |
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|
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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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|
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acesgrid.org build acesgrid web site |
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development experimental stuff |
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gcmpack an old back-up copy ? |
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gfd_lab -?- |
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manual -save- |
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misc -?- |
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mitgcm.org build web site |
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mitgcmdoc -> manual -remove- |
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models -?- |
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packages -?- |
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pdfs some pdfs |
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planetinabottle.org unfinished web site |
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preprocess -?- |
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tmp -?- |
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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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<!-- |
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<para>Efforts are underway to reduce the complexity.</para> |
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--> |
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|
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</sect2> |
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|
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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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|
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<sect2> |
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<title>Branches</title> |
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|
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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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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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|
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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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|
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<sect2> |
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<title> Developer settings </title> |
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|
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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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|
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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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|
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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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|
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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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|
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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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|
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</orderedlist> |
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|
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</sect2> |
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|
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<sect2> |
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<title>Main code development</title> |
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<para>(formerly named "Tagging" ; this section needs an update)</para> |
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|
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<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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|
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<orderedlist> |
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<listitem> |
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<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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</listitem> |
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|
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<listitem> |
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<para>The developer then runs the <ulink |
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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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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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</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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<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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url="http://mitgcm.org/viewvc/MITgcm/MITgcm/doc/tag-index"> |
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tag-index</ulink> file and checks it into the CVS |
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repository</para> |
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</listitem> |
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<listitem> |
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<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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</listitem> |
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</orderedlist> |
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</listitem> |
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</orderedlist> |
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|
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<para>The result of this tagging procedure is a sequence of development |
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checkpoints with comments which resembles:</para> |
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|
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<programlisting> |
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checkpoint50e_post |
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o make KPP work with PTRACERS |
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- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
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nearly a copy of kpp_transport_s |
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- there is no analogue to SurfaceTendencyS, so I have to use |
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gPtr(of the surface layer) instead |
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o add a new platform SunFire+mpi (SunFire 15000) to genmake |
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checkpoint50e_pre |
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|
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checkpoint50d_post |
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o change kpp output from multiple-record state files to single-record state |
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files analogous to write_state.F |
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o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
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analogous to the cg2d-related output. |
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o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
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so that writing to internal file fn (with length 512) fails. |
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checkpoint50d_pre |
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</programlisting> |
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|
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<para>This information can be used to refer to various stages of the code |
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development. For example, bugs can be traced to individual sets of CVS |
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checkins based upon their first appearance when comparing the results from |
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different checkpoints.</para> |
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|
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</sect2> |
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</sect1> |
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|
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|
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<sect1 id="coding"> |
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<title>Coding for MITgcm</title> |
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|
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<sect2 id="build_tools"> |
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<title>Build Tools</title> |
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|
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<para>Many Open Source projects use the "GNU Autotools" to help streamline |
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the build process for various Unix and Unix-like architectures. For a |
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user, the result is the common "configure" (that is, |
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"<filename>./configure && make && make install</filename>") commands. |
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For MITgcm, the process is similar. Typical commands are:</para> |
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|
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<screen> |
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$ genmake -mods=../code |
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$ make depend |
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$ make |
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</screen> |
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|
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<para>The following sections describe the individual steps in the build |
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process.</para> |
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|
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<sect3 id="genmake"> |
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<title>The <filename>genmake2</> Utility</title> |
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|
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<para><emphasis>Please note that the older <filename>genmake</> is |
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deprecated and will eventually be replaced by <filename>genmake2</>. |
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This HOWTO only describes the newer tool.</emphasis></para> |
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|
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<para>The first step in any MITgcm build is to create a Unix-style |
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<filename>Makefile</filename> which will be parsed by |
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<filename>make</filename> to specify how to compile the MITgcm source |
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files. For more detailed descriptions of what the make tools are and |
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how they are used, please see:</para> |
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|
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<itemizedlist> |
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<listitem> |
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<para><ulink url="http://www.gnu.org/software/make/make.html"> |
419 |
http://www.gnu.org/software/make/make.html</></para> |
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</listitem> |
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<listitem> |
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<para><ulink url="http://www.oreilly.com/catalog/make2/"> |
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http://www.oreilly.com/catalog/make2/</></para> |
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</listitem> |
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</itemizedlist> |
426 |
|
427 |
<para>Genmake can often be invoked successfully with a command line as |
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simple as:</para> |
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|
430 |
<screen> |
431 |
$ genmake2 -mods=../code |
432 |
</screen> |
433 |
|
434 |
<para>However, some systems (particularly commercial Unixes that lack a |
435 |
more modern "/bin/sh" implementation or that have shells installed in |
436 |
odd locations) may require an explicit shell invocation such as one of |
437 |
the following: </para> |
438 |
|
439 |
<screen> |
440 |
$ /usr/bin/sh genmake2 -make=gmake -mods=../code |
441 |
$ /opt/gnu/bin/bash genmake2 -ieee -make=/usr/local/bin/gmake -mods=../code |
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</screen> |
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|
444 |
<para>The genmake2 code has been written in a Bourne and BASH (v1) |
445 |
compatible syntax so it should work with most "sh" and all recent "bash" |
446 |
implementations.</para> |
447 |
|
448 |
<para>As the name implies, <filename>genmake2</filename> generates a |
449 |
<filename>Makefile</filename>. It does so by first parsing the |
450 |
information supplied from the following sources</para> |
451 |
|
452 |
<orderedlist> |
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<listitem> |
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<para>a <filename>gemake_local</filename> file in the current |
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directory</para> |
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</listitem> |
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<listitem> |
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<para>directly from command-line options</para> |
459 |
</listitem> |
460 |
<listitem> |
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<para>an "options file" as specified by the command-line option |
462 |
<filename>-optfile='FILENAME'</filename></para> |
463 |
</listitem> |
464 |
</orderedlist> |
465 |
|
466 |
<para>then checking certain dependency rules (the package dependencies), |
467 |
and finally writing a <filename>Makefile</filename> based upon the |
468 |
source code that it finds. For convenience within various Unix |
469 |
shells, <filename>genmake2</> supports both "long"- and "short"-style |
470 |
options. A complete list of the available options can be obtained |
471 |
from:</para> |
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|
473 |
<screen> |
474 |
$ genmake2 -help |
475 |
</screen> |
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|
477 |
<para>The most important options for <filename>genmake2</> are:</para> |
478 |
|
479 |
<variablelist> |
480 |
|
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<varlistentry> |
482 |
<term><filename>--optfile=/PATH/FILENAME</></term> |
483 |
|
484 |
<listitem> |
485 |
<para>This specifies the "options file" that should be used for a |
486 |
particular build. The options file is a convenient and |
487 |
machine-indepenent way of specifying parameters such as the |
488 |
FORTRAN compiler (<filename>FC=</>), FORTRAN compiler |
489 |
optimization flags (<filename>FFLAGS=</>), and the locations of |
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various platform- and/or machine-specific tools |
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(eg. <filename>MAKEDEPEND=</>). As with <filename>genmake2</>, |
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all options files should be written to be compatible with |
493 |
Bourne--shell ("sh" or "BASH v1") syntax. Examples of various |
494 |
options files can be found in |
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<filename>$ROOTDIR/tools/build_options</>.</para> |
496 |
|
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<para>If no "optfile" is specified (either through the command lin |
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or the environment variable), genmake2 will try to make a |
499 |
reasonable guess from the list provided in |
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<filename>$ROOTDIR/tools/build_options</>. The method used for |
501 |
making this guess is to first determine the combination of |
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operating system and hardware (eg. "linux_ia32") and then find a |
503 |
working Fortran compiler within the user's path. When these |
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three items have been identified, genmake2 will try to find an |
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optfile that has a matching name. </para> |
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|
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<para>Everyone is encouraged to submit their options files to the |
508 |
MITgcm project for inclusion (please send to |
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<email>MITgcm-support@mitgcm.org</email>). We are particularly |
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grateful for options files tested on new or unique |
511 |
platforms!</para> |
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</listitem> |
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|
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</varlistentry> |
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|
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<varlistentry> |
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<term><filename>-pdepend=/PATH/FILENAME</></term> |
518 |
|
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<listitem> |
520 |
<para>This specifies the dependency file used for packages. If |
521 |
not specified, the default dependency file is |
522 |
<filename>$ROOTDIR/pkg/pkg_depend</>. The syntax for this file is |
523 |
parsed on a line-by-line basis where each line containes either a |
524 |
comment ("#") or a simple "PKGNAME1 (+|-)PKGNAME2" pairwise rule |
525 |
where the "+" or "-" symbol specifies a "must be used with" or a |
526 |
"must not be used with" relationship, respectively. If no rule is |
527 |
specified, then it is assumed that the two packages are compatible |
528 |
and will function either with or without each other.</para> |
529 |
</listitem> |
530 |
</varlistentry> |
531 |
|
532 |
<varlistentry> |
533 |
<term><filename>-pdefault=PKG</></term> |
534 |
<term><filename>-pdefault='PKG1 [PKG2 PKG3 ...]'</></term> |
535 |
<listitem> |
536 |
<para>This option specifies the default set of packages |
537 |
to be used. If not set, the default package list will |
538 |
be read from |
539 |
<filename>$ROOTDIR/pkg/pkg_default</>.</para> |
540 |
</listitem> |
541 |
</varlistentry> |
542 |
|
543 |
<varlistentry> |
544 |
<term><filename>-adof=/path/to/file</></term> |
545 |
<term><filename>-adoptfile=/path/to/file</></term> |
546 |
<listitem> |
547 |
<para>This option specifies the "adjoint" or automatic |
548 |
differentiation options file to be used. The file is analogous |
549 |
to the "optfile" defined above but it specifies information for |
550 |
the AD build process. The default file is located in <filename> |
551 |
$ROOTDIR/tools/adjoint_options/adjoint_default </> and it |
552 |
defines the "TAF" and "TAMC" compilers. An alternate version is |
553 |
also available at <filename> |
554 |
$ROOTDIR/tools/adjoint_options/adjoint_staf </> that selects the |
555 |
newer "STAF" compiler. As with any compilers, it is helpful to |
556 |
have their directories listed in your $PATH environment |
557 |
variable.</para> |
558 |
</listitem> |
559 |
</varlistentry> |
560 |
|
561 |
<varlistentry> |
562 |
<term><filename>-mods=DIR</></term> |
563 |
<term><filename>-mods='DIR1 [DIR2 ...]'</></term> |
564 |
<listitem> |
565 |
<para>This option specifies a list of directories containing |
566 |
"modifications". These directories contain files with names |
567 |
that may (or may not) exist in the main MITgcm source tree but |
568 |
will be overridden by any identically-named sources within the |
569 |
"MODS" directories. The order of precedence for this |
570 |
"name-hiding" is as follows:</para> |
571 |
|
572 |
<itemizedlist> |
573 |
<listitem><para>"MODS" directories (in the order given) |
574 |
</para></listitem> |
575 |
<listitem><para>Packages either explicitly specified or |
576 |
provided by default (in the order given)</para></listitem> |
577 |
<listitem><para>Packages included due to package dependencies |
578 |
(in the order that that package dependencies are |
579 |
parsed)</para></listitem> |
580 |
<listitem><para>The "standard dirs" (which may have been |
581 |
specified by the "-standarddirs" option)</para></listitem> |
582 |
</itemizedlist> |
583 |
|
584 |
</listitem> |
585 |
</varlistentry> |
586 |
|
587 |
<varlistentry> |
588 |
<term><filename>-make=/path/to/gmake</></term> |
589 |
<listitem> |
590 |
<para>Due to the poor handling of soft-links and other bugs common |
591 |
with the <filename>make</> versions provided by commercial Unix |
592 |
vendors, GNU <filename>make</filename> (sometimes called |
593 |
<filename>gmake</filename>) should be preferred. This option |
594 |
provides a means for specifying the make program to be |
595 |
used.</para> |
596 |
</listitem> |
597 |
</varlistentry> |
598 |
|
599 |
</variablelist> |
600 |
|
601 |
<para>A successful run of <filename>genmake2</> will produce a |
602 |
<filename>Makefile</>, a <filename>PACKAGES_CONFIG.h</> file, and |
603 |
various convenience files used for the automatic differentiation |
604 |
process.</para> |
605 |
|
606 |
<para>In general, it is best to use <filename>genmake2</> on a "clean" |
607 |
directory that is free of all source (*.[F,f],*.[F,f]90) and header |
608 |
(*.h,*.inc) files. Generally, this can be accomplished in an |
609 |
"un-clean" directory by running "make CLEAN" followed by "make |
610 |
makefile".</para> |
611 |
|
612 |
</sect3> |
613 |
|
614 |
<sect3 id="makefile_use"> |
615 |
<title>Using the <filename>Makefile</></title> |
616 |
|
617 |
<para>Once a <filename>Makefile</> has been created using |
618 |
<filename>genmake2</>, one can build a "standard" (forward |
619 |
simulator) executable using:</para> |
620 |
|
621 |
<screen> |
622 |
$ make CLEAN |
623 |
$ make depend |
624 |
$ make |
625 |
</screen> |
626 |
|
627 |
<para>The "make CLEAN" step will remove any stale source files, include |
628 |
files, and links. It is strongly recommended for "un-clean" |
629 |
directories which may contain the (perhaps partial) results of |
630 |
previous builds. Such "debris" can interfere with the next stage of |
631 |
the build.</para> |
632 |
|
633 |
<para>The "make depend" step will create a large number of symbolic |
634 |
links from the local directory to the source file locations. It also |
635 |
parses these files and creates an extensive list of dependencies |
636 |
within the <filename>Makefile</> itself. The links that exist at this |
637 |
stage are mostly "large F" files (*.F and *.F90) that need to be |
638 |
processed by a C preprocessor ("CPP"). Since "make depend" edits the |
639 |
<filename>Makefile</>, it is important not to skip this step!</para> |
640 |
|
641 |
<para>The final "make" invokes the C preprocessor to produce the "little |
642 |
f" files (*.f and *.f90) and then compiles them to object code using |
643 |
the specified FORTRAN compiler and options. An intermediate script is |
644 |
often used during this stage to further process (usually, make simple |
645 |
substitutions) custom definitions such as variable types within the |
646 |
source files. This additional stage is necessary in order to overcome |
647 |
some of the inconsistencies in the sizes of objects (bytes) between |
648 |
different compilers. The result of the build process is an executable |
649 |
with the name <filename>mitgcmuv</>.</para> |
650 |
|
651 |
<para>In addition to the forward simulator described above, the |
652 |
<filename>Makefile</> also has a number of targets that can be used to |
653 |
produce various adjoint and tangent-linear builds for optimization and |
654 |
other parameter-sensitivity problems. The additional targets within |
655 |
the <filename>Makefile</> are:</para> |
656 |
|
657 |
<variablelist> |
658 |
|
659 |
<varlistentry> |
660 |
<term><filename>make adall</></term> |
661 |
<listitem> |
662 |
<para>This target produces an <filename>mitgcmuv_ad</> executable |
663 |
using the <filename>taf</> or <filename>staf</> adjoint |
664 |
compiler. See the <filename>genmake2</> "-adof" option for |
665 |
compiler selection.</para> |
666 |
</listitem> |
667 |
</varlistentry> |
668 |
|
669 |
<varlistentry> |
670 |
<term><filename>make ftlall</></term> |
671 |
<listitem> |
672 |
<para>Similar to <filename>make adall</> above, this |
673 |
produces...</para> |
674 |
</listitem> |
675 |
</varlistentry> |
676 |
|
677 |
</variablelist> |
678 |
|
679 |
<para>Please report any compilation failures or other build problems to |
680 |
the <email>MITgcm-support@mitgcm.org</email> list.</para> |
681 |
|
682 |
</sect3> |
683 |
|
684 |
</sect2> |
685 |
|
686 |
<sect2 id="verification"> |
687 |
<title>The Verification Suite</title> |
688 |
|
689 |
<para>The MITgcm CVS tree (within the <filename>$ROOTDIR/verification/</> |
690 |
directory) includes more than a dozen examples intended for regression |
691 |
testing. Each one of these example directories contains "known-good" |
692 |
output files along with all the input (including both code and data |
693 |
files) required for their re-calculation. These example directories are |
694 |
further broken down into sets of subdirectories |
695 |
(eg. <filename>/input</>, <filename>/code</>) intended to expedite the |
696 |
testing process.</para> |
697 |
|
698 |
<sect3 id="testreport"> |
699 |
<title>The <filename>testreport</> Utility</title> |
700 |
|
701 |
<para>Also included in <filename>$ROOTDIR/verification/</> are shell |
702 |
scripts for automated testing. The newest script (which was written |
703 |
to work with <filename>genmake2</>) is called <filename>testreport</>. |
704 |
This script can be used to build different versions of the MITgcm |
705 |
code, run the various examples, compare the output, and (if specified) |
706 |
email the results of each one of these tests to a central |
707 |
repository.</para> |
708 |
|
709 |
<para>On some systems, the testreport script can be run with a command |
710 |
line as simple as:</para> |
711 |
|
712 |
<screen> |
713 |
$ cd verification |
714 |
$ ./testreport -ieee |
715 |
</screen> |
716 |
|
717 |
<para>However, some systems (those lacking or wiht a broken "/bin/sh") |
718 |
may require an explicit shell invocation such as:</para> |
719 |
|
720 |
<screen> |
721 |
$ sh ./testreport -ieee -t 'exp0 exp4' |
722 |
$ /some/path/to/bash ./testreport -ieee -t 'ideal_2D_oce lab_sea natl_box' |
723 |
</screen> |
724 |
|
725 |
<para>The <filename>testreport</> script accepts a number of |
726 |
command-line options which can be listed using the <filename>-help</> |
727 |
option. The most important ones are:</para> |
728 |
|
729 |
<variablelist> |
730 |
|
731 |
<varlistentry> |
732 |
<term><filename>-ieee</></term> |
733 |
<listitem> |
734 |
<para>If allowed by the compiler (as defined in the "optfile"), |
735 |
use IEEE arithmetic. This option, along with the GCC compiler, |
736 |
is how the standard results were produced.</para> |
737 |
</listitem> |
738 |
</varlistentry> |
739 |
|
740 |
<varlistentry> |
741 |
<term><filename>-tdir TESTDIR</></term> |
742 |
<term><filename>-tdir 'TDIR1 TDIR2 [...]'</></term> |
743 |
<listitem> |
744 |
<para>This option specifies the test directory or list of test |
745 |
directories that should be used. Each of these entries should |
746 |
exactly (note: they are case sensitive!) match the names of |
747 |
directries in <filename>$ROOTDIR/verification/</>. If this |
748 |
option is omitted, then all directories that are properly |
749 |
formatted (that is, containing an <filename>input</> |
750 |
sub-directory and a <filename>results/output.txt</> file) will |
751 |
be used.</para> |
752 |
</listitem> |
753 |
</varlistentry> |
754 |
|
755 |
<varlistentry> |
756 |
<term><filename>-optfile=/PATH/FILENAME</></term> |
757 |
<term><filename>-optfile '/PATH/F1 [/PATH/F2 ...]'</></term> |
758 |
<listitem> |
759 |
<para>This specifies a list of "options files" that will be passed |
760 |
to <filename>genmake2</>. If multiple options files are used |
761 |
(say, to test different compilers or different sets of options |
762 |
for the same compiler), then each options file will be used with |
763 |
each of the test directories.</para> |
764 |
</listitem> |
765 |
</varlistentry> |
766 |
|
767 |
<varlistentry> |
768 |
<term><filename>-addr EMAIL</></term> |
769 |
<term><filename>-addr 'EMAIL1 EMAIL2 [...]'</></term> |
770 |
<listitem> |
771 |
<para>Send the results (namely, <filename>output.txt</>, |
772 |
<filename>genmake_local</>, <filename>genmake_state</>, and |
773 |
<filename>Makefile</>) to the specified email addresses. The |
774 |
results are gzipped, placed in a tar file, MIME encoded, and |
775 |
sent to the specified address. If no email addresses are |
776 |
specified, no mail is sent.</para> |
777 |
</listitem> |
778 |
</varlistentry> |
779 |
|
780 |
<varlistentry> |
781 |
<term><filename>-mpi</></term> |
782 |
<listitem> |
783 |
<para>If the necessary files |
784 |
(<filename>TESTDIR/code/CPP_EEOPTIONS.h_mpi</> and |
785 |
<filename>TESTDIR/code/SIZE.h_mpi</>) exist, then use them for an |
786 |
MPI--enabled run. Note that the use of MPI typically requires a |
787 |
special command option (see "-command" below) to invoke the MPI |
788 |
executable. Examples of PBS scripts using MPI with testreport can be |
789 |
found in the <ulink |
790 |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/"> |
791 |
MITgcm-contrib area</ulink></para> |
792 |
</listitem> |
793 |
</varlistentry> |
794 |
|
795 |
<varlistentry> |
796 |
<term><filename>-command='some command to run'</></term> |
797 |
<listitem> |
798 |
<para>For some tests, particularly MPI runs, the default "make |
799 |
output.txt" is not sufficient. This option allows a more general |
800 |
command (or shell script) to be invoked. Examples of PBS scripts |
801 |
using MPI with testreport can be found in the <ulink |
802 |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/"> |
803 |
MITgcm-contrib area</ulink></para> |
804 |
</listitem> |
805 |
</varlistentry> |
806 |
|
807 |
</variablelist> |
808 |
|
809 |
<para>The <filename>testreport</> script will write progress to the |
810 |
screen (stdout) as it runs. In addition, it will create a |
811 |
<filename>tr_out.txt</> file that contains a brief comparison of the |
812 |
current output with the "known-good" output.</para> |
813 |
|
814 |
</sect3> |
815 |
|
816 |
</sect2> |
817 |
|
818 |
|
819 |
<sect2 id="packages"> |
820 |
<title>Creating MITgcm Packages</title> |
821 |
|
822 |
<para>Optional parts of code have been separated from the MITgcmUV core |
823 |
driver code and organised into packages. The packaging structure |
824 |
provides a mechanism for maintaining suites of code, specific to |
825 |
particular classes of problems, in a way that is cleanly separated from |
826 |
the generic fluid dynamical engine.</para> |
827 |
|
828 |
<para>The MITgcmUV packaging structure is described below using generic |
829 |
package names ${pkg}. A concrete examples of a package is the code for |
830 |
implementing GM/Redi mixing. This code uses the package name</para> |
831 |
|
832 |
</sect2> |
833 |
|
834 |
</sect1> |
835 |
|
836 |
<sect1> |
837 |
<title>Chris's Notes...</title> |
838 |
|
839 |
<programlisting> |
840 |
MITgcmUV Packages |
841 |
================= |
842 |
|
843 |
Optional parts of code are separated from |
844 |
the MITgcmUV core driver code and organised into |
845 |
packages. The packaging structure provides a mechanism for |
846 |
maintaining suites of code, specific to particular |
847 |
classes of problem, in a way that is cleanly |
848 |
separated from the generic fluid dynamical engine. |
849 |
|
850 |
The MITgcmUV packaging structure is describe |
851 |
below using generic package names ${pkg}. |
852 |
A concrete examples of a package is the code |
853 |
for implementing GM/Redi mixing. This code uses |
854 |
the package name |
855 |
* ${PKG} = GMREDI |
856 |
* ${pkg} = gmredi |
857 |
* ${Pkg} = gmRedi |
858 |
|
859 |
Package states |
860 |
============== |
861 |
|
862 |
Packages can be any one of four states, included, |
863 |
excluded, enabled, disabled as follows: |
864 |
|
865 |
included(excluded) compile time state which |
866 |
includes(excludes) package |
867 |
code and routine calls from |
868 |
compilation/linking etc... |
869 |
|
870 |
enabled(disabled) run-time state which |
871 |
enables(disables) package code |
872 |
execution. |
873 |
|
874 |
Every call to a ${pkg}_... routine from outside the package |
875 |
should be placed within both a |
876 |
#ifdef ALLOW_${PKG} ... block and a |
877 |
if ( use${Pkg} ) ... then block. |
878 |
Package states are generally not expected to change during |
879 |
a model run. |
880 |
|
881 |
Package structure |
882 |
================= |
883 |
|
884 |
o Each package gets its runtime configuration |
885 |
parameters from a file named "data.${pkg}" |
886 |
Package runtime config. options are imported |
887 |
into a common block held in a header file |
888 |
called "${PKG}.h". |
889 |
Note: In some packages, the header file "${PKG}.h" is splitted |
890 |
into "${PKG}_PARAMS.h" that contains the package parameters and |
891 |
${PKG}_VARS.h" for the field arrays. |
892 |
|
893 |
o The core driver part of the model can check |
894 |
for runtime enabling or disabling of individual packages |
895 |
through logical flags use${Pkg}. |
896 |
The information is loaded from a |
897 |
global package setup file called "data.pkg". |
898 |
The use${Pkg} flags are not used within |
899 |
individual packages. |
900 |
|
901 |
o Included in "${PKG}.h" is a logical flag |
902 |
called ${Pkg}IsOn. The "${PKG}.h" header file can be imported |
903 |
by other packages to check dependencies and requirements |
904 |
from other packages ( see "Package Boot Sequence" section). |
905 |
NOTE: This procedure is not presently implemented, |
906 |
----- neither for kpp nor for gmRedi. |
907 |
|
908 |
CPP Flags |
909 |
========= |
910 |
|
911 |
1. Within the core driver code flags of the form |
912 |
ALLOW_${PKG} are used to include or exclude |
913 |
whole packages. The ALLOW_${PKG} flags are included |
914 |
from a PACKAGES_CONFIG.h file that is automatically |
915 |
generated by genmake2 (see genmake2 section). |
916 |
held in-line in the CPP_OPTIONS.h header file. |
917 |
e.g. |
918 |
|
919 |
Core model code ..... |
920 |
|
921 |
#include "PACKAGES_CONFIG.h" |
922 |
#include "CPP_OPTIONS.h" |
923 |
: |
924 |
: |
925 |
: |
926 |
|
927 |
#ifdef ALLOW_${PKG} |
928 |
if ( use${Pkg} ) CALL ${PKG}_DO_SOMETHING(...) |
929 |
#endif |
930 |
|
931 |
2. Within an individual package a header file, |
932 |
"${PKG}_OPTIONS.h", is used to set CPP flags |
933 |
specific to that package. It also includes |
934 |
"PACKAGES_CONFIG.h" and "CPP_OPTIONS.h". |
935 |
|
936 |
|
937 |
Package Boot Sequence |
938 |
===================== |
939 |
|
940 |
Calls to package routines within the core code timestepping |
941 |
loop can vary. However, all packages follow a required |
942 |
"boot" sequence outlined here: |
943 |
|
944 |
1. S/R PACKAGES_BOOT() |
945 |
: |
946 |
CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... ) |
947 |
|
948 |
|
949 |
2. S/R PACKAGES_READPARMS() |
950 |
: |
951 |
#ifdef ALLOW_${PKG} |
952 |
if ( use${Pkg} ) |
953 |
& CALL ${PKG}_READPARMS( retCode ) |
954 |
#endif |
955 |
|
956 |
3. S/R PACKAGES_INIT_FIXED() |
957 |
: |
958 |
#ifdef ALLOW_${PKG} |
959 |
if ( use${Pkg} ) |
960 |
& CALL ${PKG}_INIT_FIXED( retCode ) |
961 |
#endif |
962 |
|
963 |
4. S/R PACKAGES_CHECK() |
964 |
: |
965 |
#ifdef ALLOW_${PKG} |
966 |
if ( use${Pkg} ) |
967 |
& CALL ${PKG}_CHECK( retCode ) |
968 |
#else |
969 |
if ( use${Pkg} ) |
970 |
& CALL PACKAGES_CHECK_ERROR('${PKG}') |
971 |
#endif |
972 |
|
973 |
5. S/R PACKAGES_INIT_VARIABLES() |
974 |
: |
975 |
#ifdef ALLOW_${PKG} |
976 |
if ( use${Pkg} ) |
977 |
& CALL ${PKG}_INIT_VARIA( ) |
978 |
#endif |
979 |
|
980 |
Package Output |
981 |
============== |
982 |
6. S/R DO_THE_MODEL_IO |
983 |
|
984 |
#ifdef ALLOW_${PKG} |
985 |
if ( use${Pkg} ) |
986 |
& CALL ${PKG}_OUTPUT( ) |
987 |
#endif |
988 |
|
989 |
7. S/R PACKAGES_WRITE_PICKUP() |
990 |
|
991 |
#ifdef ALLOW_${PKG} |
992 |
if ( use${Pkg} ) |
993 |
& CALL ${PKG}_WRITE_PICKUP( ) |
994 |
#endif |
995 |
|
996 |
Description |
997 |
=========== |
998 |
|
999 |
- ${PKG}_READPARMS() |
1000 |
is responsible for reading |
1001 |
in the package parameters file data.${pkg}, and storing |
1002 |
the package parameters in "${PKG}.h" (or in "${PKG}_PARAMS.h"). |
1003 |
-> called from INITIALISE_FIXED in PACKAGES_READPARMS |
1004 |
|
1005 |
- ${PKG}_INIT_FIXED() |
1006 |
is responsible for completing the internal setup of a package. |
1007 |
-> called from INITIALISE_FIXED in PACKAGES_INIT_FIXED |
1008 |
note: 1) some pkg use instead: |
1009 |
CALL ${PKG}_INITIALISE ( or the old form CALL ${PKG}_INIT ) |
1010 |
2) for simple pkg setup, this part is done inside ${PKG}_READPARMS |
1011 |
|
1012 |
- ${PKG}_CHECK() |
1013 |
is responsible for validating |
1014 |
basic package setup and inter-package dependencies. |
1015 |
${PKG}_CHECK can import other package parameters it may |
1016 |
need to check. This is done through header files "${PKG}.h". |
1017 |
It is assumed that parameters owned by other packages |
1018 |
will not be reset during ${PKG}_CHECK(). |
1019 |
-> called from INITIALISE_FIXED in PACKAGES_CHECK |
1020 |
|
1021 |
- ${PKG}_INIT_VARIA() |
1022 |
is responsible for fill-in all package variables with an initial value. |
1023 |
Contains eventually a call to ${PKG}_READ_PICKUP that will read |
1024 |
from a pickup file the package variables required to restart the model. |
1025 |
This routine is called after the core model state has been completely |
1026 |
initialised but before the core model timestepping starts. |
1027 |
-> called from INITIALISE_VARIA in PACKAGES_INIT_VARIABLES |
1028 |
note: the name ${PKG}_INIT_VARIA is not yet standard and some pkg |
1029 |
use for e.g. ${PKG}_INI_VARS, ${PKG}_INIT_VARIABLES, or the old |
1030 |
form ${PKG}_INIT |
1031 |
|
1032 |
- ${PKG}_OUTPUT( ) |
1033 |
is responsible for writing time-average fields to output files |
1034 |
(but the cumulating step is done within the package main S/R). |
1035 |
Can also contain other diagnostics (.e.g. CALL ${PKG}_MONITOR) |
1036 |
and write snap-shot fields that are hold in common blocks. Other |
1037 |
temporary fields are directly dump to file where they are available. |
1038 |
NOTE: 1) the S/R old name ${PKG}_DIAGS is used in some packages |
1039 |
but is beeing replaced by ${PKG}_OUTPUT |
1040 |
to avoid confusion with pkg/diagnostics functionality. |
1041 |
2) the output part is not yet in a standard form and might still |
1042 |
evolve a lot. |
1043 |
-> called within DO_THE_MODEL_IO |
1044 |
|
1045 |
- ${PKG}_WRITE_PICKUP() |
1046 |
is responsible for writing a package pickup file when necessary for |
1047 |
a restart. (found also the old name: ${PKG}_WRITE_CHECKPOINT ) |
1048 |
-> called from FORWARD_STEP and THE_MODEL_MAIN in PACKAGES_WRITE_PICKUP |
1049 |
|
1050 |
Summary |
1051 |
======= |
1052 |
|
1053 |
- CPP options: |
1054 |
----------------------- |
1055 |
* ALLOW_${PKG} include/exclude package for compilation |
1056 |
|
1057 |
- FORTRAN logical: |
1058 |
----------------------- |
1059 |
* use${Pkg} enable package for execution at runtime |
1060 |
-> declared in PARAMS.h |
1061 |
* ${Pkg}IsOn for package cross-dependency check |
1062 |
-> declared in ${PKG}.h |
1063 |
N.B.: Not presently used! |
1064 |
|
1065 |
- header files |
1066 |
----------------------- |
1067 |
* ${PKG}_OPTIONS.h has further package-specific CPP options |
1068 |
* ${PKG}.h package-specific common block variables, fields |
1069 |
or ${PKG}_PARAMS.h package-specific common block parameters |
1070 |
and ${PKG}_VARS.h package-specific common block fields |
1071 |
|
1072 |
- FORTRAN source files |
1073 |
----------------------- |
1074 |
* ${pkg}_readparms.F reads parameters from file data.${pkg} |
1075 |
* ${pkg}_init_fixed.F complete the package setup |
1076 |
* ${pkg}_check.F checks package dependencies and consistencies |
1077 |
* ${pkg}_init_varia.F initialises package-related fields |
1078 |
* ${pkg}_... .F package source code |
1079 |
* ${pkg}_output.F write output to file. |
1080 |
* ${pkg}_write_pickup.F write a package pickup file to restart the model |
1081 |
|
1082 |
New: Subroutine in one package (pkgA) that only contains code which |
1083 |
is connected to a 2nd package (pkgB) (e.g.: gmredi_diagnostics_init.F) |
1084 |
will be named: pkgA_pkgB_something.F |
1085 |
|
1086 |
- parameter file |
1087 |
----------------------- |
1088 |
* data.${pkg} parameter file |
1089 |
</programlisting> |
1090 |
|
1091 |
</sect1> |
1092 |
|
1093 |
|
1094 |
<sect1 id="documentation"> |
1095 |
<title>Editing the Documentation</title> |
1096 |
|
1097 |
<sect2 id="documentation_getting"> |
1098 |
<title>Getting the Docs and Code</title> |
1099 |
|
1100 |
<para>The first step towards editing the documentation is to checkout a |
1101 |
copy of code, docs, and build scripts from the CVS server using:</para> |
1102 |
|
1103 |
<screen> |
1104 |
$ export CVS_RSH=ssh |
1105 |
$ export CVSROOT=':ext:NAME@mitgcm.org:/u/gcmpack' |
1106 |
$ mkdir scratch |
1107 |
$ cvs co -P MITgcm manual mitgcm.org |
1108 |
</screen> |
1109 |
|
1110 |
<para>These commands extract the necessary information from the CVS server |
1111 |
and create a temporary (called <filename>scratch</filename>) directory for |
1112 |
the storage of the HTML and other files that will be created. Please note |
1113 |
that you must either create <filename>scratch</filename> as shown or edit |
1114 |
the various <filename>Makefile</filename>s and scripts used to create the |
1115 |
documentation.</para> |
1116 |
</sect2> |
1117 |
|
1118 |
<sect2> |
1119 |
<title>Editing the Documentation</title> |
1120 |
|
1121 |
<para>The documentation is contained in the <filename>manual</filename> |
1122 |
directory in a raw LaTeX format. The main document is |
1123 |
<filename>manual.tex</filename> and it uses <command>\input{}</command>s |
1124 |
to include the chapters and subsections.</para> |
1125 |
|
1126 |
<para>Since the same LaTeX source is used to produce PostScript, PDF, and |
1127 |
HTML output, care should be taken to follow certain conventions. Two of |
1128 |
the most important are the usage of the <command>\filelink{}{}</command> |
1129 |
and <command>\varlink{}{}</command> commands. Both of these commands have |
1130 |
been defined to simplify the connection between the automatically |
1131 |
generated ("code browser") HTML and the HTML version of the manual |
1132 |
produced by LaTeX2HTML. They each take two arguments (corresponding to |
1133 |
the contents of the two sets of curly braces) which are the text that the |
1134 |
author wishes to be "wrapped" within the link, and a specially formatted |
1135 |
link thats relative to the <filename>MITgcm</filename> directory within |
1136 |
the CVS tree.</para> |
1137 |
|
1138 |
<para>The result is a command that resembles either</para> |
1139 |
|
1140 |
<orderedlist> |
1141 |
<listitem> |
1142 |
<para>a reference to a variable or subroutine name such as |
1143 |
<command>\varlink{tRef}{tRef}</command>, or </para> |
1144 |
</listitem> |
1145 |
|
1146 |
<listitem> |
1147 |
<para>a reference to a file such as |
1148 |
<command>\varlink{tRef}{path-to-the-file_name.F}</command> |
1149 |
where the absolute path to the file is of the form |
1150 |
<filename>/foo/MITgcm/path/to/the/file_name.F</filename></para> |
1151 |
<para>(please note how the leading "/foo/MITgcm" |
1152 |
component of the path is dropped leaving the path |
1153 |
<emphasis>relative</emphasis> to the head of the code |
1154 |
directory and each directory separator "/" is turned |
1155 |
into a "-")</para> |
1156 |
</listitem> |
1157 |
</orderedlist> |
1158 |
|
1159 |
|
1160 |
|
1161 |
</sect2> |
1162 |
|
1163 |
<sect2> |
1164 |
<title>Building the Documentation</title> |
1165 |
|
1166 |
<para>Given the directory structure of <xref |
1167 |
linkend="documentation_getting">, the entire documentation for the web |
1168 |
site can be built using:</para> |
1169 |
|
1170 |
<screen> |
1171 |
$ cd mitgcm.org/devel/buildweb |
1172 |
$ make All |
1173 |
</screen> |
1174 |
|
1175 |
<para>Which builds the PDF from the LaTeX source, creates the HTML output |
1176 |
from the LaTeX source, parses the FORTRAN code base to produce a |
1177 |
hyperlinked HTML version of the source, and then determines the |
1178 |
cross-linking between the various HTML components.</para> |
1179 |
|
1180 |
<para>If there are no errors, the result of the build process (which can |
1181 |
take 30+ minutes on a P4/2.5Ghz) will be contained within a single |
1182 |
directory called <filename>scratch/dev_docs</filename>. This is a freshly |
1183 |
built version of the entire on-line users manual. If you have the correct |
1184 |
permissions, it can be directly copied to the web server area:</para> |
1185 |
|
1186 |
<screen> |
1187 |
$ mv scratch/dev_docs /u/u0/httpd/html |
1188 |
</screen> |
1189 |
|
1190 |
<para>and the update is complete.</para> |
1191 |
|
1192 |
</sect2> |
1193 |
|
1194 |
</sect1> |
1195 |
|
1196 |
</article> |