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<article id="MITgcm-Development-HOWTO"> |
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<article id="MITgcm-Development-HOWTO"> |
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<articleinfo> |
<articleinfo> |
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<title>MITgcm Development HOWTO</title> |
<title>MITgcm Development HOWTO</title> |
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Initial version. |
Initial version. |
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</revremark> |
</revremark> |
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</revision> |
</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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<revision> |
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<revnumber>0.04</revnumber> |
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<date>2011-04-24</date> |
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<authorinitials>jmc</authorinitials> |
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<revremark> |
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Update subsection "The verification suite". |
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</revremark> |
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</revision> |
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</revhistory> |
</revhistory> |
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<abstract> |
<abstract> |
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<sect2> |
<sect2> |
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<title>New Versions of This Document</title> <para>You can |
<title>New Versions of This Document</title> <para>You can |
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obtain the latest version of this document <ulink |
obtain the latest version of this document <ulink |
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url="http://mitgcm.org/dev_docs/devel_HOWTO/">online</ulink> in |
url="http://mitgcm.org/public/docs.html">online</ulink> in |
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various formats.</para> |
various formats.</para> |
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</sect2> |
</sect2> |
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<sect2> |
<sect2> |
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<sect2> |
<sect2> |
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<title>User Manual</title> |
<title>User Manual</title> |
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<para>Before jumping into |
<para>Before jumping into development, please familiarize yourself with |
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development, please familiarize yourself with the MITgcm user |
the <ulink url="http://mitgcm.org/public/docs.html"> MITgcm user manual |
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manual which is available <ulink |
</ulink>. This document contains volumes of useful information and is |
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url="http://mitgcm.org/">on the main web page</ulink>. This |
included here by reference.</para> |
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document contains volumes of useful information and is included |
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here by reference.</para> |
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<para>Also, a "snapshot" or<ulink |
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<para>Also, a "snapshot" or <ulink |
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url="http://mitgcm.org/dev_docs/">development version</ulink> of |
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 |
the user manual may be available, though this is only put on the |
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web for testing purposes.</para> |
web for testing purposes.</para> |
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--> |
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</sect2> |
</sect2> |
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<sect2> |
<sect2> |
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<sect1 id="cvs"> |
<sect1 id="cvs"> |
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<title>CVS Repository</title> |
<title>CVS Repository</title> |
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<sect2> |
<sect2> |
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<title>Layout</title> |
<title>Layout</title> |
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others. The tree currently resembles:</para> |
others. The tree currently resembles:</para> |
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<programlisting>gcmpack/ |
<programlisting>gcmpack/ |
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MITgcm-contrib contributed code |
CVSROOT -hidden- |
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CS-regrid goes into utils |
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cvspolicy.html -save- |
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CVSROOT -save- |
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development experimental stuff |
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manual -save- |
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misc -?- |
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MITgcm code |
MITgcm code |
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adjoint fold into genmake |
bin empty |
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bin stub for ecco build |
doc basic developpment documentation |
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compare01 old from 20th century |
eesupp execution environment support code (wrapper) |
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diags timeave f77 in pkgs now |
exe empty |
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doc tags -- connect to real docs? |
jobs runtime shell scripts for |
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eesupp cnh? |
various platforms (not maintained) |
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exe ecco user build |
lsopt line search |
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,- jobs runtime shell scripts for |
model main dynamics (core) |
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| various platforms |
optim line search interface |
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| lsopt line search |
pkg alternate and optional numerics, etc. |
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m| model main dynamics (core) |
tools scripts to build (and test) |
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e| optimization_drivers ? |
utils pre/post processing tools (matlab, ..) |
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r| optim line search interface |
verification standard regression tests + examples |
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g| pkg alternate and optional numerics, etc. |
+ documented examples (tutorials) |
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e|- tools |
tutorial_examples (only in release1 branch) |
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?| tutorial_examples documented tests |
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| only populated on release1 branch |
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| and not validated during "testscript" |
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'- utils |
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verification std tests |
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MITgcm_contrib contributed code |
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mitgcmdoc -> manual -remove- |
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 |
mitgcm.org build web site |
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models -?- |
old_develop old and early development source |
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packages -?- |
misc -?- |
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preprocess -?- |
models -?- |
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tmp -?- |
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> |
</programlisting> |
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<para>Efforts are underway to reduce the complexity.</para> |
<para>Efforts are underway to reduce the complexity.</para> |
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--> |
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</sect2> |
</sect2> |
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<title>Branches</title> |
<title>Branches</title> |
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<para>As shown in the online <ulink |
<para>As shown in the online <ulink |
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url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/doc/tag-index?graph=1.174">ViewCVS-generated |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm/model/src/forward_step.F?view=graph"> |
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tree</ulink>, the MITgcm codebase is split into to two branches |
ViewCVS-generated tree</ulink>, the MITgcm codebase is split into |
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or "lines" under which development proceeds. These two lines |
branches or "lines" under which development proceeds. The main line |
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are referred to as the "MAIN" and "ecco" versions of the code. |
of development is referred to as the "MAIN" version of the code. |
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While not identical, the bulk of the MAIN and ecco lines are |
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composed of files from the same codebase. |
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</para> |
</para> |
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<para>Periodically, a "Release" branch is formed from the "MAIN" |
<para>Periodically, a "Release" branch is formed from the "MAIN" |
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development branch. This is done in order to create a |
development branch. This is done in order to create a relatively stable |
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relatively stable reference point for both users and developers. |
reference point for both users and developers. The intent is that once a |
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The intent is that once a relese branch has been created, only |
release branch has been created, only bug-fixes will be added to it. |
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bug-fixes will be added to it. Meanwhile, development (which |
Meanwhile, development (which might "break" or otherwise render invalid |
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might "break" or otherwise render invalid the documentation, |
the documentation, tutorials, and/or examples contained within a release |
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tutorials, and/or examples contained within a release branch) is |
branch) is allowed to continue along the MAIN line.</para> |
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allowed to continue along the MAIN and ecco lines.</para> |
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</sect2> |
</sect2> |
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<sect2> |
<sect2> |
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<title>Tagging</title> |
<title> Developer settings </title> |
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<para>The intent of tagging is to create "known-good" |
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checkpoints that developers can use as references. |
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Traditionally, MITgcm tagging has maintained the following |
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conventions:</para> |
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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> |
<orderedlist> |
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<listitem> |
<listitem> |
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<para>Developer checks out code into a local CVS-managed |
<para> You will need an account (login access) to the server |
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directory, makes various changes/additions, tests these |
"mitgcm.org" (curently: <filename>forge.csail.mit.edu</filename>) |
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edits, and eventually reaches a point where (s)he is |
with the proper group setting (e.g., group "gcmctrb" to add/modify |
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satisfied that the changes form a new "useful" point in the |
code into MITgcm_contrib). |
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evolution of the code.</para> |
This kind of account is granted only upon well motivated request |
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(we recommend to ask your senior MITgcm-collaborator to send such |
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request to marshall-admin at techsquare.com with Cc to Chris Hill |
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for approval).</para> |
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<para> The access to the server <filename>mitgcm.org</filename> is |
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through ssh-key authorization which will need to be set properly on |
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both side (on your local machine and on your server account). |
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You need to be able to ssh to <filename>mitgcm.org</filename> |
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(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 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 CVS-anonymous mode (using "cvsanon", |
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as mentionned <ulink url="http://mitgcm.org/public/source_code.html"> |
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here </ulink>) does not provide 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> The reason for such limitation is that when downloading a directory, |
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e.g.: <filename>myCopy</filename>, 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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This prevent 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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<para> Note: |
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Please ignore the following warnings that the "cvs commit" command |
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produces if you are not part of the "gcmpack" group: |
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<screen> |
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cvs commit: failed to create lock directory for `/u/gcmpack/CVSROOT' |
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(/u/gcmpack/CVSROOT/#cvs.history.lock): Permission denied |
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cvs commit: failed to obtain history lock in repository `/u/gcmpack' |
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</screen> |
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These warnings are not affecting the changes you made to the CVS repository. |
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</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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<para><emphasis>(formerly named "Tagging" ; this section needs an update) |
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</emphasis></para> |
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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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<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> |
</listitem> |
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<listitem> |
<listitem> |
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<para>The developer then runs the <ulink |
<para>The developer then runs the <ulink |
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url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/verification/testscript">testscript</ulink> |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm/verification/testreport"> |
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shell script to see if any problems are introduced. While |
testreport</ulink> shell script to see if any problems are introduced. |
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not intended to be exhaustive, the test cases within the |
While not intended to be exhaustive, the test cases within the |
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verification directory do provide some indication whether |
verification directory do provide some indication whether gross errors |
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gross errors have been introduced. |
have been introduced. |
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</para> |
</para> |
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</listitem> |
</listitem> |
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then:</para> |
then:</para> |
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<orderedlist> |
<orderedlist> |
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<listitem> |
<listitem> |
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<para>adds a "checkpointXY_pre" comment (where X is a |
<para>adds a "checkpointXY_pre" comment (where X is a checkpoint |
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checkpoint number and Y is a letter) to the <ulink |
number and Y is a letter) to the <ulink |
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url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/doc/tag-index">tag-index</ulink> |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm/doc/tag-index"> |
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file and checks it into the CVS repository</para> |
tag-index</ulink> file and checks it into the CVS |
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repository</para> |
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</listitem> |
</listitem> |
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<listitem> |
<listitem> |
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<para>submits the set of changes to the CVS repository |
<para>submits the set of changes to the CVS repository and adds |
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and adds comments to <filename>tag-index</filename> |
comments to <filename>tag-index</filename> describing what the |
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describing what the changes are along with a matching |
changes are along with a matching "checkpointXY_post" entry</para> |
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"checkpointXY_post" entry</para> |
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</listitem> |
</listitem> |
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</orderedlist> |
</orderedlist> |
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</listitem> |
</listitem> |
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</orderedlist> |
</orderedlist> |
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<para>The result of this tagging procedure is a sequence of |
<para>The result of this tagging procedure is a sequence of development |
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development checkpoints with comments which resembles:</para> |
checkpoints with comments which resembles:</para> |
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<programlisting> |
<programlisting> |
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checkpoint50e_post |
checkpoint50e_post |
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o make KPP work with PTRACERS |
o make KPP work with PTRACERS |
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- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
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nearly a copy of kpp_transport_s |
nearly a copy of kpp_transport_s |
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- there is no analogue to SurfaceTendencyS, so I have to use |
- there is no analogue to SurfaceTendencyS, so I have to use |
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gPtr(of the surface layer) instead |
gPtr(of the surface layer) instead |
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o add a new platform SunFire+mpi (SunFire 15000) to genmake |
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
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checkpoint50e_pre |
checkpoint50e_pre |
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checkpoint50d_post |
checkpoint50d_post |
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o change kpp output from multiple-record state files to single-record state |
o change kpp output from multiple-record state files to single-record state |
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files analogous to write_state.F |
files analogous to write_state.F |
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o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
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analogous to the cg2d-related output. |
analogous to the cg2d-related output. |
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o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
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. |
so that writing to internal file fn (with length 512) fails. |
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checkpoint50d_pre |
checkpoint50d_pre |
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</programlisting> |
</programlisting> |
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<para>This information can be used to refer to various stages of |
<para>This information can be used to refer to various stages of the code |
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the code development. For example, bugs can be traced to |
development. For example, bugs can be traced to individual sets of CVS |
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individual sets of CVS checkins based upon their first |
checkins based upon their first appearance when comparing the results from |
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appearance when comparing the results from different |
different checkpoints.</para> |
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checkpoints.</para> |
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</sect2> |
</sect2> |
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</sect1> |
</sect1> |
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<sect1 id="documentation"> |
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<title>Editing the Documentation</title> |
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<sect2 id="documentation_getting"> |
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<title>Getting the Docs and Code</title> |
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<para>The first step towards editing the documentation is to |
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checkout a copy of code, docs, and build scripts from the CVS |
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server using:</para> |
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<screen> |
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$ export CVS_RSH=ssh |
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$ export CVSROOT=':ext:auden.lcs.mit.edu:/u/u3/gcmpack' |
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$ mkdir scratch |
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$ cvs co MITgcm manual mitgcm.org |
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</screen> |
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<para>These commands extract the necessary information from the |
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CVS server and create a temporary (called |
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<filename>scratch</filename>) directory for the storage of the |
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HTML and other files that will be created. Please note that you |
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must either create <filename>scratch</filename> as shown or edit |
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the various <filename>Makefile</filename>s and scripts used to |
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create the documentation.</para> |
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</sect2> |
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<sect2> |
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<title>Editing the Documentation</title> |
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<para>The documentation is contained in the |
|
|
<filename>manual</filename> directory in a raw LaTeX format. |
|
|
The main document is <filename>manual.tex</filename> and it uses |
|
|
<command>\input{}</command>s to include the chapters and |
|
|
subsections.</para> |
|
|
|
|
|
<para>Since the same LaTeX source is used to produce PostScript, |
|
|
PDF, and HTML output, care should be taken to follow certain |
|
|
conventions. Two of the most important are the usage of the |
|
|
<command>\filelink{}{}</command> and |
|
|
<command>\varlink{}{}</command> commands. Both of these |
|
|
commands have been defined to simplify the connection between |
|
|
the automatically generated ("code browser") HTML and the HTML |
|
|
version of the manual produced by LaTeX2HTML. They each take |
|
|
two arguments (corresponding to the contents of the two sets of |
|
|
curly braces) which are the text that the author wishes to be |
|
|
"wrapped" within the link, and a specially formatted link thats |
|
|
relative to the <filename>MITgcm</filename> directory within the |
|
|
CVS tree.</para> |
|
|
|
|
|
<para>The result is a command that resembles either</para> |
|
|
|
|
|
<orderedlist> |
|
|
<listitem> |
|
|
<para>a reference to a variable or subroutine name such as |
|
|
<command>\varlink{tRef}{tRef}</command>, or </para> |
|
|
</listitem> |
|
|
|
|
|
<listitem> |
|
|
<para>a reference to a file such as |
|
|
<command>\varlink{tRef}{path-to-the-file_name.F}</command> |
|
|
where the absolute path to the file is of the form |
|
|
<filename>/foo/MITgcm/path/to/the/file_name.F</filename></para> |
|
|
<para>(please note how the leading "/foo/MITgcm" |
|
|
component of the path is dropped leaving the path |
|
|
<emphasis>relative</emphasis> to the head of the code |
|
|
directory and each directory separator "/" is turned |
|
|
into a "-")</para> |
|
|
</listitem> |
|
|
</orderedlist> |
|
|
|
|
|
|
|
|
|
|
|
</sect2> |
|
|
|
|
|
<sect2> |
|
|
<title>Building the Documentation</title> |
|
|
|
|
|
<para>Given the directory structure of <xref |
|
|
linkend="documentation_getting">, the entire documentation for the web |
|
|
site can be built using:</para> |
|
|
|
|
|
<screen> |
|
|
$ cd mitgcm.org/devel/buildweb |
|
|
$ make All |
|
|
</screen> |
|
|
|
|
|
<para>Which builds the PDF from the LaTeX source, creates the |
|
|
HTML output from the LaTeX source, parses the FORTRAN code base |
|
|
to produce a hyperlinked HTML version of the source, and then |
|
|
determines the cross-linking between the various HTML |
|
|
components.</para> |
|
|
|
|
|
<para>If there are no errors, the result of the build process |
|
|
(which can take 30+ minutes on a P4/2.5Ghz) will be contained |
|
|
within a single directory called |
|
|
<filename>scratch/dev_docs</filename>. This is a freshly built |
|
|
version of the entire on-line users manual. If you have the |
|
|
correct permissions, it can be directly copied to the web server |
|
|
area:</para> |
|
|
|
|
|
<screen> |
|
|
$ mv scratch/dev_docs /u/u0/httpd/html |
|
|
</screen> |
|
|
|
|
|
<para>and the update is complete.</para> |
|
|
|
|
|
</sect2> |
|
|
|
|
|
</sect1> |
|
|
|
|
407 |
<sect1 id="coding"> |
<sect1 id="coding"> |
408 |
<title>Coding for MITgcm</title> |
<title>Coding for MITgcm</title> |
409 |
|
|
417 |
For MITgcm, the process is similar. Typical commands are:</para> |
For MITgcm, the process is similar. Typical commands are:</para> |
418 |
|
|
419 |
<screen> |
<screen> |
420 |
$ genmake -mods=../code |
$ genmake2 -mods=../code |
421 |
$ make depend |
$ make depend |
422 |
$ make |
$ make |
423 |
</screen> |
</screen> |
424 |
|
|
425 |
<para>The following sections describe the individual steps in the build |
<para>The following sections describe the individual steps in the build |
426 |
process.</para> |
process.</para> |
427 |
|
|
428 |
<sect3 id="genmake"> |
<sect3 id="genmake"> |
429 |
<title>The <filename>genmake2</> Utility</title> |
<title>The <filename>genmake2</> Utility</title> |
430 |
|
|
431 |
<para><emphasis>Please note that the older <filename>genmake</> is |
<para><emphasis>(Note: the older <filename>genmake</> |
432 |
deprecated and will eventually be replaced by <filename>genmake2</>. |
has been replaced by <filename>genmake2</>)</emphasis></para> |
|
This HOWTO only describes the newer tool.</emphasis></para> |
|
433 |
|
|
434 |
<para>The first step in any MITgcm build is to create a Unix-style |
<para>The first step in any MITgcm build is to create a Unix-style |
435 |
<filename>Makefile</filename> which will be parsed by |
<filename>Makefile</filename> which will be parsed by |
452 |
simple as:</para> |
simple as:</para> |
453 |
|
|
454 |
<screen> |
<screen> |
455 |
$ genmake2 -mods=../code |
$ genmake2 -mods=../code |
456 |
</screen> |
</screen> |
457 |
|
|
458 |
<para>However, some systems (particularly commercial Unixes that lack a |
<para>However, some systems (particularly commercial Unixes that lack a |
461 |
the following: </para> |
the following: </para> |
462 |
|
|
463 |
<screen> |
<screen> |
464 |
$ /usr/bin/sh genmake2 -make=gmake -mods=../code |
$ /usr/bin/sh genmake2 -make=gmake -mods=../code |
465 |
$ /opt/gnu/bin/bash genmake2 -ieee -make=/usr/local/bin/gmake -mods=../code |
$ /opt/gnu/bin/bash genmake2 -ieee -make=/usr/local/bin/gmake -mods=../code |
466 |
</screen> |
</screen> |
467 |
|
|
468 |
<para>The genmake2 code has been written in a Bourne and BASH (v1) |
<para>The genmake2 code has been written in a Bourne and BASH (v1) |
475 |
|
|
476 |
<orderedlist> |
<orderedlist> |
477 |
<listitem> |
<listitem> |
478 |
<para>a <filename>gm_local</filename> file in the current |
<para>a <filename>gemake_local</filename> file in the current |
479 |
directory</para> |
directory</para> |
480 |
</listitem> |
</listitem> |
481 |
<listitem> |
<listitem> |
485 |
<para>an "options file" as specified by the command-line option |
<para>an "options file" as specified by the command-line option |
486 |
<filename>-optfile='FILENAME'</filename></para> |
<filename>-optfile='FILENAME'</filename></para> |
487 |
</listitem> |
</listitem> |
488 |
|
<listitem> |
489 |
|
<para> a <filename>packages.conf</filename> file (in the current |
490 |
|
directory or in one of the "MODS" directories, see below) |
491 |
|
which contains the specific list of packages to compile |
492 |
|
</para> |
493 |
|
</listitem> |
494 |
</orderedlist> |
</orderedlist> |
495 |
|
|
496 |
<para>then checking certain dependency rules (the package dependencies), |
<para>then checking certain dependency rules (the package dependencies), |
501 |
from:</para> |
from:</para> |
502 |
|
|
503 |
<screen> |
<screen> |
504 |
$ genmake2 -help |
$ genmake2 -help |
505 |
</screen> |
</screen> |
506 |
|
|
507 |
<para>The most important options for <filename>genmake2</> are:</para> |
<para>The most important options for <filename>genmake2</> are:</para> |
544 |
</varlistentry> |
</varlistentry> |
545 |
|
|
546 |
<varlistentry> |
<varlistentry> |
547 |
<term><filename>-pdepend=/PATH/FILENAME</></term> |
<term><filename>-adof=/path/to/file</></term> |
548 |
|
<term><filename>-adoptfile=/path/to/file</></term> |
|
<listitem> |
|
|
<para>This specifies the dependency file used for packages. If |
|
|
not specified, the default dependency file is |
|
|
<filename>$ROOTDIR/pkg/pkg_depend</>. The syntax for this file is |
|
|
parsed on a line-by-line basis where each line containes either a |
|
|
comment ("#") or a simple "PKGNAME1 (+|-)PKGNAME2" pairwise rule |
|
|
where the "+" or "-" symbol specifies a "must be used with" or a |
|
|
"must not be used with" relationship, respectively. If no rule is |
|
|
specified, then it is assumed that the two packages are compatible |
|
|
and will function either with or without each other.</para> |
|
|
</listitem> |
|
|
|
|
|
</varlistentry> |
|
|
|
|
|
<varlistentry> |
|
|
<term><filename>-pdefault=PKG</></term> |
|
|
<term><filename>-pdefault='PKG1 [PKG2 PKG3 ...]'</></term> |
|
549 |
<listitem> |
<listitem> |
550 |
<para>This option specifies the default set of packages |
<para>This option specifies the "adjoint" or automatic |
551 |
to be used. If not set, the default package list will |
differentiation options file to be used. The file is analogous |
552 |
be read from |
to the "optfile" defined above but it specifies information for |
553 |
<filename>$ROOTDIR/pkg/pkg_default</>.</para> |
the AD build process. The default file is located in <filename> |
554 |
|
$ROOTDIR/tools/adjoint_options/adjoint_default </> and it |
555 |
|
defines the "TAF" and "TAMC" compilers. An alternate version is |
556 |
|
also available at <filename> |
557 |
|
$ROOTDIR/tools/adjoint_options/adjoint_staf </> that selects the |
558 |
|
newer "STAF" compiler. As with any compilers, it is helpful to |
559 |
|
have their directories listed in your $PATH environment |
560 |
|
variable.</para> |
561 |
</listitem> |
</listitem> |
562 |
</varlistentry> |
</varlistentry> |
563 |
|
|
571 |
will be overridden by any identically-named sources within the |
will be overridden by any identically-named sources within the |
572 |
"MODS" directories. The order of precedence for this |
"MODS" directories. The order of precedence for this |
573 |
"name-hiding" is as follows:</para> |
"name-hiding" is as follows:</para> |
|
|
|
574 |
<itemizedlist> |
<itemizedlist> |
575 |
<listitem><para>"MODS" directories (in the order given) |
<listitem><para>"MODS" directories (in the order given) |
576 |
</para></listitem> |
</para></listitem> |
577 |
<listitem><para>Packages either explicitly specified or |
<listitem><para>Packages either explicitly specified or |
578 |
provided by default (in the order given)</para></listitem> |
provided by default (in the order given)</para></listitem> |
579 |
<listitem><para>Packages included due to package dependencies |
<listitem><para>Packages included due to package dependencies |
580 |
(in the order that that package dependencies are |
(in the order that that package dependencies are |
581 |
parsed)</para></listitem> |
parsed)</para></listitem> |
582 |
<listitem><para>The "standard dirs" (which may have been |
<listitem><para>The "standard dirs" (which may have been |
583 |
specified by the "-standarddirs" option)</para></listitem> |
specified by the "-standarddirs" option)</para></listitem> |
584 |
</itemizedlist> |
</itemizedlist> |
585 |
|
</listitem> |
586 |
|
</varlistentry> |
587 |
|
|
588 |
|
<varlistentry> |
589 |
|
<term><filename>-pgroups=/PATH/FILENAME</></term> |
590 |
|
<listitem> |
591 |
|
<para>This option specifies the file where package groups are |
592 |
|
defined. If not set, the package-groups definition will |
593 |
|
be read from |
594 |
|
<filename>$ROOTDIR/pkg/pkg_groups</>.</para> |
595 |
|
<para> |
596 |
|
It also contains the default list of packages (defined |
597 |
|
as the group <filename>"default_pkg_list"</>) which is used |
598 |
|
when no specific package list (file: <filename>packages.conf</>) |
599 |
|
is found in current directory or in any "MODS" directory. |
600 |
|
</para> |
601 |
|
</listitem> |
602 |
|
</varlistentry> |
603 |
|
|
604 |
|
<varlistentry> |
605 |
|
<term><filename>-pdepend=/PATH/FILENAME</></term> |
606 |
|
|
607 |
|
<listitem> |
608 |
|
<para>This specifies the dependency file used for packages. If |
609 |
|
not specified, the default dependency file is |
610 |
|
<filename>$ROOTDIR/pkg/pkg_depend</>. The syntax for this file is |
611 |
|
parsed on a line-by-line basis where each line containes either a |
612 |
|
comment ("#") or a simple "PKGNAME1 (+|-)PKGNAME2" pairwise rule |
613 |
|
where the "+" or "-" symbol specifies a "must be used with" or a |
614 |
|
"must not be used with" relationship, respectively. If no rule is |
615 |
|
specified, then it is assumed that the two packages are compatible |
616 |
|
and will function either with or without each other.</para> |
617 |
</listitem> |
</listitem> |
618 |
</varlistentry> |
</varlistentry> |
619 |
|
|
639 |
<para>In general, it is best to use <filename>genmake2</> on a "clean" |
<para>In general, it is best to use <filename>genmake2</> on a "clean" |
640 |
directory that is free of all source (*.[F,f],*.[F,f]90) and header |
directory that is free of all source (*.[F,f],*.[F,f]90) and header |
641 |
(*.h,*.inc) files. Generally, this can be accomplished in an |
(*.h,*.inc) files. Generally, this can be accomplished in an |
642 |
"un-clean" directory by running "make CLEAN" followed by "make |
"un-clean" directory by running "make Clean" followed by "make |
643 |
makefile".</para> |
makefile".</para> |
644 |
|
|
645 |
</sect3> |
</sect3> |
646 |
|
|
647 |
<sect3 id="makefile_use"> |
<sect3 id="makefile_use"> |
648 |
<title>Using <filename>Makefile</></title> |
<title>Using the <filename>Makefile</></title> |
649 |
|
|
650 |
<para>Once a <filename>Makefile</> has been created, one can |
<para>Once a <filename>Makefile</> has been created using |
651 |
build an executable using:</para> |
<filename>genmake2</>, one can build a "standard" (forward |
652 |
|
simulator) executable using:</para> |
653 |
|
|
654 |
<screen> |
<screen> |
655 |
$ make CLEAN |
$ make Clean |
656 |
$ make depend |
$ make depend |
657 |
$ make |
$ make |
658 |
</screen> |
</screen> |
659 |
|
|
660 |
<para>The "make CLEAN" step will remove any stale source files, include |
<para>The "make Clean" step will remove any stale source files, include |
661 |
files, and links. It is strongly recommended for "un-clean" |
files, and links. It is strongly recommended for "un-clean" |
662 |
directories which may contain the (perhaps partial) results of |
directories which may contain the (perhaps partial) results of |
663 |
previous builds. Such "debris" can interfere with the next stage of |
previous builds. Such "debris" can interfere with the next stage of |
664 |
the build.</para> |
the build. |
665 |
|
A more agressive cleaning option, "make CLEAN", can be used to also |
666 |
|
remove the executable and output files from a previous run.</para> |
667 |
|
|
668 |
<para>The "make depend" step will create a large number of symbolic |
<para>The "make depend" step will create a large number of symbolic |
669 |
links from the local directory to the source file locations. It also |
links from the local directory to the source file locations. It also |
680 |
substitutions) custom definitions such as variable types within the |
substitutions) custom definitions such as variable types within the |
681 |
source files. This additional stage is necessary in order to overcome |
source files. This additional stage is necessary in order to overcome |
682 |
some of the inconsistencies in the sizes of objects (bytes) between |
some of the inconsistencies in the sizes of objects (bytes) between |
683 |
different compilers.</para> |
different compilers. The result of the build process is an executable |
684 |
|
with the name <filename>mitgcmuv</>.</para> |
685 |
|
|
686 |
<para>Please report compilation failures or other problems to |
<para>In addition to the forward simulator described above, the |
687 |
<email>MITgcm-support@mitgcm.org</email>.</para> |
<filename>Makefile</> also has a number of targets that can be used to |
688 |
|
produce various adjoint and tangent-linear builds for optimization and |
689 |
|
other parameter-sensitivity problems. The additional targets within |
690 |
|
the <filename>Makefile</> are:</para> |
691 |
|
|
692 |
|
<variablelist> |
693 |
|
|
694 |
|
<varlistentry> |
695 |
|
<term><filename>make adall</></term> |
696 |
|
<listitem> |
697 |
|
<para>This target produces an <filename>mitgcmuv_ad</> executable |
698 |
|
using the <filename>taf</> or <filename>staf</> adjoint |
699 |
|
compiler. See the <filename>genmake2</> "-adof" option for |
700 |
|
compiler selection.</para> |
701 |
|
</listitem> |
702 |
|
</varlistentry> |
703 |
|
|
704 |
|
<varlistentry> |
705 |
|
<term><filename>make ftlall</></term> |
706 |
|
<listitem> |
707 |
|
<para>Similar to <filename>make adall</> above, this |
708 |
|
produces...</para> |
709 |
|
</listitem> |
710 |
|
</varlistentry> |
711 |
|
|
712 |
|
</variablelist> |
713 |
|
|
714 |
|
<para>Please report any compilation failures or other build problems to |
715 |
|
the <email>MITgcm-support@mitgcm.org</email> list.</para> |
716 |
|
|
717 |
</sect3> |
</sect3> |
718 |
|
|
722 |
<title>The Verification Suite</title> |
<title>The Verification Suite</title> |
723 |
|
|
724 |
<para>The MITgcm CVS tree (within the <filename>$ROOTDIR/verification/</> |
<para>The MITgcm CVS tree (within the <filename>$ROOTDIR/verification/</> |
725 |
directory) includes more than a dozen examples intended for regression |
directory) includes many (> 90) examples intended for regression |
726 |
testing. Each one of these example directories contains "known-good" |
testing. Each one of these test-experiment directories contains "known-good" |
727 |
output files along with all the input (including both code and data |
output files along with all the input (including both code and data |
728 |
files) required for their re-calculation. These example directories are |
files) required for their re-calculation. |
729 |
further broken down into sets of subdirectories |
Also included in <filename>$ROOTDIR/verification/</> is the shell |
730 |
(eg. <filename>/input</>, <filename>/code</>) intended to expedite the |
script <filename>testreport</> to perform regression tests.</para> |
731 |
testing process.</para> |
|
732 |
|
<sect3 id="test-experiment"> |
733 |
|
<title>Test-experiment Directory Content</title> |
734 |
|
|
735 |
|
<para> Each test-experiment directory (<filename>TESTDIR</>) contains |
736 |
|
several standard subdirectories and files which <filename>testreport</> |
737 |
|
recognizes and uses when running a regression test. |
738 |
|
The directories/files that <filename>testreport</> uses are different |
739 |
|
for a forward test and an adjoint test (<filename>testreport -adm</>) |
740 |
|
and some test-experiments are set-up for only one type of regression |
741 |
|
test whereas others allow both types of tests (forward and adjoint).</para> |
742 |
|
<para>Also some test-experiment allows, using the same MITgcm executable, |
743 |
|
to perform multiple tests using different parameters and input files, |
744 |
|
with a primary input set-up |
745 |
|
(<filename>input/ </> or <filename>input_ad/ </>) |
746 |
|
and corresponding results (<filename>results/output.txt</> or |
747 |
|
<filename>results/output_adm.txt</>) and with one or several secondary |
748 |
|
inputs (<filename>input.OTHER/ </> or <filename>input_ad.OTHER/ </>) |
749 |
|
and corresponding results (<filename>results/output.OTHER.txt </> |
750 |
|
or <filename>results/output_adm.OTHER.txt</>).</para> |
751 |
|
<variablelist> |
752 |
|
|
753 |
|
<varlistentry> |
754 |
|
<term>directory <filename>TESTDIR/results/</></term> |
755 |
|
<listitem> |
756 |
|
<para>contains reference standard output used for test comparison. |
757 |
|
<filename>results/output.txt</> and |
758 |
|
<filename>results/output_adm.txt</> |
759 |
|
correspond respectively to primary forward and adjoint test |
760 |
|
run on the reference platform (currently |
761 |
|
<filename>baudelaire.csail.mit.edu</>) |
762 |
|
on one processor (no MPI, single thread) |
763 |
|
using the reference compiler (curently the GNU fortran |
764 |
|
compiler <filename>gfortran</>). |
765 |
|
The presence of these files determines whether or not |
766 |
|
<filename>testreport</> is testing or skipping |
767 |
|
this test-experiment. |
768 |
|
Reference standard output for secondary tests |
769 |
|
(<filename>results/output.OTHER.txt</> |
770 |
|
or <filename>results/output_adm.OTHER.txt</>) are |
771 |
|
also expected here.</para> |
772 |
|
<para>The test comparison involves few model variables output, which are, |
773 |
|
by default and for a forward test, the 2-D solver initial residual |
774 |
|
(<filename>cg2d_init_res</>) and 3-D state variables (T,S,U,V) |
775 |
|
monitor output, and, by default and for an adjoint test, the |
776 |
|
cost-function and gradient-check. However, some test-experiments |
777 |
|
use some package-specific variable/monitor output according to |
778 |
|
the file <filename>TESTDIR/input[_ad][.OTHER]/tr_checklist</> |
779 |
|
specification.</para> |
780 |
|
</listitem> |
781 |
|
</varlistentry> |
782 |
|
|
783 |
|
<varlistentry> |
784 |
|
<term>directory <filename>TESTDIR/build/</></term> |
785 |
|
<listitem> |
786 |
|
<para> initially empty directory where <filename>testreport</> |
787 |
|
will build the MITgcm executable for forward and adjoint test. |
788 |
|
It might contains an experiment specific |
789 |
|
<filename>genmake_local</> file (see <xref linkend="genmake">). |
790 |
|
</para> |
791 |
|
<para> Note that the original <filename>code[_ad]/SIZE.h_mpi</> |
792 |
|
is not directly used as "SIZE.h" to build an MPI-executable ; |
793 |
|
instead, a local copy <filename>build/SIZE.h.mpi</> is derived |
794 |
|
from <filename>code[_ad]/SIZE.h_mpi</> |
795 |
|
by adjusting the number of processors (nPx,nPy) according to |
796 |
|
<filename>NUMBER_OF_PROCS</> (see <xref linkend="testreport">, |
797 |
|
<filename>testreport -MPI</>) ; then it is linked to "SIZE.h" |
798 |
|
(<filename> ln -s SIZE.h.mpi SIZE.h </>) before building |
799 |
|
the MPI-executable.</para> |
800 |
|
</listitem> |
801 |
|
</varlistentry> |
802 |
|
|
803 |
|
<varlistentry> |
804 |
|
<term>directory <filename>TESTDIR/code/</></term> |
805 |
|
<listitem> |
806 |
|
<para>contains the test-experiment specific source code |
807 |
|
used to build the MITgcm executable (<filename>mitgcmuv</>) |
808 |
|
for forward-test (using <filename>genmake2 -mods=../code</>). |
809 |
|
</para> |
810 |
|
<para> It can also contain specific source files with the suffix |
811 |
|
"<filename>_mpi</>" to be used |
812 |
|
<!-- |
813 |
|
in the <filename>TESTDIR/build/</> directory |
814 |
|
--> |
815 |
|
in place of the corresponding file (without suffix) |
816 |
|
for an MPI test (see <xref linkend="testreport">). |
817 |
|
The presence or absence of <filename>SIZE.h_mpi</> |
818 |
|
determines whether or not an MPI test on this |
819 |
|
test-experiment is performed or skipped.</para> |
820 |
|
</listitem> |
821 |
|
</varlistentry> |
822 |
|
|
823 |
|
<varlistentry> |
824 |
|
<term>directory <filename>TESTDIR/code_ad/</></term> |
825 |
|
<listitem> |
826 |
|
<para>contains the test-experiment specific source code |
827 |
|
used to build the MITgcm executable (<filename>mitgcmuv_ad</>) |
828 |
|
for adjoint-test (using <filename>genmake2 -mods=../code_ad</>). |
829 |
|
It can also contain specific source files with the suffix |
830 |
|
"<filename>_mpi</>" (see above).</para> |
831 |
|
</listitem> |
832 |
|
</varlistentry> |
833 |
|
|
834 |
|
<varlistentry> |
835 |
|
<term>directory <filename>TESTDIR/input/</></term> |
836 |
|
<listitem> |
837 |
|
<para>contains the input and parameter files |
838 |
|
used to run the primary forward test of this test-experiment. |
839 |
|
</para> |
840 |
|
<para>It can also contain specific parameter files with the suffix |
841 |
|
"<filename>.mpi</>" to be used |
842 |
|
<!-- |
843 |
|
in the <filename>TESTDIR/run/</> directory |
844 |
|
--> |
845 |
|
in place of the corresponding file (without suffix) for MPI |
846 |
|
test, or with suffix "<filename>.mth</>" to be used for |
847 |
|
multi-threaded test (see <xref linkend="testreport">). |
848 |
|
The presence or absence of <filename>eedata.mth</> |
849 |
|
determines whether or not a multi-threaded test on this |
850 |
|
test-experiment is performed or skipped.</para> |
851 |
|
<para>To save disk space and reduce downloading time, multiple |
852 |
|
copies of the same input file is avoided by using a shell |
853 |
|
script <filename>prepare_run</>. |
854 |
|
When such a script is found in <filename>TESTDIR/input/ </>, |
855 |
|
<filename>testreport</> run this script in directory |
856 |
|
<filename>TESTDIR/run/ </> after linking all the input file |
857 |
|
from <filename>TESTDIR/input/ </>. |
858 |
|
</para> |
859 |
|
</listitem> |
860 |
|
</varlistentry> |
861 |
|
|
862 |
|
<varlistentry> |
863 |
|
<term>directory <filename>TESTDIR/input_ad/</></term> |
864 |
|
<listitem> |
865 |
|
<para>contains the input and parameter files |
866 |
|
used to run the primary adjoint test of this test-experiment. |
867 |
|
It can also contain specific parameter files with the suffix |
868 |
|
"<filename>.mpi</>" and shell script <filename>prepare_run</> |
869 |
|
as described above.</para> |
870 |
|
</listitem> |
871 |
|
</varlistentry> |
872 |
|
|
873 |
|
<varlistentry> |
874 |
|
<term>directory <filename>TESTDIR/input.OTHER/</></term> |
875 |
|
<listitem> |
876 |
|
<para>contains the input and parameter files |
877 |
|
used to run the secondary OTHER forward test of this test-experiment. |
878 |
|
It can also contain specific parameter files with suffix |
879 |
|
"<filename>.mpi</>" or "<filename>.mth</>" and shell script |
880 |
|
<filename>prepare_run</> (see above).</para> |
881 |
|
<para> The presence or absence the file <filename>eedata.mth</> |
882 |
|
determines whether or not a secondary multi-threaded test on this |
883 |
|
test-experiment is performed or skipped.</para> |
884 |
|
</listitem> |
885 |
|
</varlistentry> |
886 |
|
|
887 |
|
<varlistentry> |
888 |
|
<term>directory <filename>TESTDIR/input_ad.OTHER/</></term> |
889 |
|
<listitem> |
890 |
|
<para>contains the input and parameter files |
891 |
|
used to run the secondary OTHER adjoint test of this test-experiment. |
892 |
|
It can also contain specific parameter files with the suffix |
893 |
|
"<filename>.mpi</>" and shell script <filename>prepare_run</> |
894 |
|
(see above).</para> |
895 |
|
</listitem> |
896 |
|
</varlistentry> |
897 |
|
<!-- |
898 |
|
--> |
899 |
|
<varlistentry> |
900 |
|
<term>directory <filename>TESTDIR/run/</></term> |
901 |
|
<listitem> |
902 |
|
<para> initially empty directory where <filename>testreport</> |
903 |
|
will run the MITgcm executable for primary forward and adjoint |
904 |
|
test.</para> |
905 |
|
<para>Symbolic links (using command "<filename>ln -s</>") are made |
906 |
|
for input and parameter files (from <filename>../input/ </> |
907 |
|
or from <filename>../input_ad/ </>) and for MITgcm executable |
908 |
|
(from <filename>../build/ </>) before the run proceeds. |
909 |
|
The sequence of links (function <filename>linkdata</> within shell |
910 |
|
script <filename>testreport</>) for a forward test is:</para> |
911 |
|
<screen> |
912 |
|
* link+rename or remove links |
913 |
|
to special files with suffix ".mpi" or ".mth" from ../input/ |
914 |
|
* link files from ../input/ |
915 |
|
* execute ../input/prepare_run (if it exists) |
916 |
|
</screen> |
917 |
|
<para>The sequence for an ajoint test is similar, with |
918 |
|
<filename>../input_ad/ </> replacing <filename>../input/ </>. |
919 |
|
</para> |
920 |
|
</listitem> |
921 |
|
</varlistentry> |
922 |
|
|
923 |
|
<varlistentry> |
924 |
|
<term>directory <filename>TESTDIR/tr_run.OTHER/</></term> |
925 |
|
<listitem> |
926 |
|
<para> directory created by <filename>testreport</> |
927 |
|
to run the MITgcm executable for secondary "OTHER" forward |
928 |
|
or adjoint test.</para> |
929 |
|
<para> The sequence of links for a forward secondary test is:</para> |
930 |
|
<screen> |
931 |
|
* link+rename or remove links |
932 |
|
to special files with suffix ".mpi" or ".mth" from ../input.OTHER/ |
933 |
|
* link files from ../input.OTHER/ |
934 |
|
* execute ../input.OTHER/prepare_run (if it exists) |
935 |
|
* link files from ../input/ |
936 |
|
* execute ../input/prepare_run (if it exists) |
937 |
|
</screen> |
938 |
|
<para>The sequence for an ajoint test is similar, with |
939 |
|
<filename>../input_ad.OTHER/ </> and <filename>../input_ad/ </> |
940 |
|
replacing <filename>../input.OTHER/ </> and <filename>../input/ </>. |
941 |
|
</para> |
942 |
|
</listitem> |
943 |
|
</varlistentry> |
944 |
|
|
945 |
|
</variablelist> |
946 |
|
</sect3> |
947 |
|
|
948 |
<sect3 id="testreport"> |
<sect3 id="testreport"> |
949 |
<title>The <filename>testreport</> Utility</title> |
<title>The <filename>testreport</> Utility</title> |
950 |
|
|
951 |
<para>Also included in <filename>$ROOTDIR/verification/</> are shell |
<para> The shell script <filename>testreport</> (in |
952 |
scripts for automated testing. The newest script (which was written |
<filename>$ROOTDIR/verification/</>), which was written to work with |
953 |
to work with <filename>genmake2</>) is called <filename>testreport</>. |
<filename>genmake2</>, can be used to build different versions |
954 |
This script can be used to build different versions of the MITgcm |
of the MITgcm code, run the various examples, compare the output, |
955 |
code, run the various examples, compare the output, and (if specified) |
and (if specified) email the results of each one of these tests to a |
956 |
email the results of each one of these tests to a central |
central repository.</para> |
|
repository.</para> |
|
957 |
|
|
958 |
<para>On some systems, the testreport script can be run with a command |
<para>On some systems, the testreport script can be run with a command |
959 |
line as simple as:</para> |
line as simple as:</para> |
960 |
|
|
961 |
<screen> |
<screen> |
962 |
$ cd verification |
$ cd verification |
963 |
$ ./testreport -ieee |
$ ./testreport |
964 |
</screen> |
</screen> |
965 |
|
|
966 |
<para>However, some systems (those lacking or wiht a broken "/bin/sh") |
<para>However, some systems (those lacking or wiht a broken "/bin/sh") |
967 |
may require an explicit shell invocation such as:</para> |
may require an explicit shell invocation such as:</para> |
968 |
|
|
969 |
<screen> |
<screen> |
970 |
$ sh ./testreport -ieee -t 'exp0 exp4' |
$ sh ./testreport -t 'exp2 exp4' |
971 |
$ /some/path/to/bash ./testreport -ieee -t 'ideal_2D_oce lab_sea natl_box' |
$ /some/path/to/bash ./testreport -t 'ideal_2D_oce lab_sea natl_box' |
972 |
</screen> |
</screen> |
973 |
|
|
974 |
<para>The <filename>testreport</> script accepts a number of |
<para>The <filename>testreport</> script accepts a number of |
978 |
<variablelist> |
<variablelist> |
979 |
|
|
980 |
<varlistentry> |
<varlistentry> |
981 |
<term><filename>-ieee</></term> |
<term><filename>-ieee</> (default) / <filename>-noieee</></term> |
982 |
<listitem> |
<listitem> |
983 |
<para>If allowed by the compiler (as defined in the "optfile"), |
<para>If allowed by the compiler (as defined in the "optfile"), |
984 |
use IEEE arithmetic. This option, along with the GCC compiler, |
use IEEE arithmetic (<filename>genmake2 -ieee</>). |
985 |
is how the standard results were produced.</para> |
This option, along with the gfortran / gcc compiler, |
986 |
|
is how the standard results are produced.</para> |
987 |
|
</listitem> |
988 |
|
</varlistentry> |
989 |
|
|
990 |
|
<varlistentry> |
991 |
|
<term><filename>-optfile=/PATH/FILENAME</></term> |
992 |
|
<term><filename>-optfile '/PATH/F1 [/PATH/F2 ...]'</></term> |
993 |
|
<listitem> |
994 |
|
<para>This specifies a list of "options files" that will be passed |
995 |
|
to <filename>genmake2</>. If multiple options files are used |
996 |
|
(say, to test different compilers or different sets of options |
997 |
|
for the same compiler), then each options file will be used with |
998 |
|
each of the test directories.</para> |
999 |
</listitem> |
</listitem> |
1000 |
</varlistentry> |
</varlistentry> |
1001 |
|
|
1006 |
<para>This option specifies the test directory or list of test |
<para>This option specifies the test directory or list of test |
1007 |
directories that should be used. Each of these entries should |
directories that should be used. Each of these entries should |
1008 |
exactly (note: they are case sensitive!) match the names of |
exactly (note: they are case sensitive!) match the names of |
1009 |
directries in <filename>$ROOTDIR/verification/</>. If this |
directories in <filename>$ROOTDIR/verification/</>. If this |
1010 |
option is omitted, then all directories that are properly |
option is omitted, then all directories that are properly |
1011 |
formatted (that is, containing an <filename>input</> |
formatted (that is, containing an <filename>input</> |
1012 |
sub-directory and a <filename>results/output.txt</> file) will |
sub-directory and a <filename>results/output.txt</> file) will |
1015 |
</varlistentry> |
</varlistentry> |
1016 |
|
|
1017 |
<varlistentry> |
<varlistentry> |
|
<term><filename>-optfile=/PATH/FILENAME</></term> |
|
|
<term><filename>-optfile '/PATH/F1 [/PATH/F2 ...]'</></term> |
|
|
<listitem> |
|
|
<para>This specifies a list of "options files" that will be passed |
|
|
to <filename>genmake2</>. If multiple options files are used |
|
|
(say, to test different compilers or different sets of options |
|
|
for the same compiler), then each options file will be used with |
|
|
each of the test directories.</para> |
|
|
</listitem> |
|
|
</varlistentry> |
|
|
|
|
|
<varlistentry> |
|
1018 |
<term><filename>-addr EMAIL</></term> |
<term><filename>-addr EMAIL</></term> |
1019 |
<term><filename>-addr 'EMAIL1 EMAIL2 [...]'</></term> |
<term><filename>-addr 'EMAIL1 EMAIL2 [...]'</></term> |
1020 |
<listitem> |
<listitem> |
1028 |
</varlistentry> |
</varlistentry> |
1029 |
|
|
1030 |
<varlistentry> |
<varlistentry> |
1031 |
|
<term><filename>-MPI NUMBER_OF_PROCS</></term> |
1032 |
<term><filename>-mpi</></term> |
<term><filename>-mpi</></term> |
1033 |
<listitem> |
<listitem> |
1034 |
<para>If the necessary files |
<para>If the necessary file (<filename>TESTDIR/code/SIZE.h_mpi</>) |
1035 |
(<filename>TESTDIR/code/CPP_EEOPTIONS.h_mpi</> and |
exists, then use it (and all <filename>TESTDIR/code/*_mpi</> files) |
1036 |
<filename>TESTDIR/code/SIZE.h_mpi</>) exist, then use them for an |
for an MPI--enabled run. The new option (<filename>-MPI</> followed |
1037 |
MPI--enabled run. Note that the use of MPI typically requires a |
by the maximum number of processors) enable to build and run each |
1038 |
|
test-experiment using variable number of MPI processors (multiple |
1039 |
|
of <filename>nPx*nPy</> from <filename>TESTDIR/code/SIZE.h_mpi</> |
1040 |
|
and not larger than <filename>NUMBER_OF_PROCS</>). |
1041 |
|
The short option ("-mpi") can only be used to build and run on 2 MPI |
1042 |
|
processors (equivalent to "<filename>-MPI 2</>").</para> |
1043 |
|
<para>Note that the use of MPI typically requires a |
1044 |
special command option (see "-command" below) to invoke the MPI |
special command option (see "-command" below) to invoke the MPI |
1045 |
executable. Examples of PBS scripts using MPI with testreport can be |
executable. Examples of PBS scripts using testreport with MPI can be |
1046 |
found in the <ulink |
found in the <ulink |
1047 |
url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/"> |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/"> |
1048 |
MITgcm-contrib area</ulink></para> |
tools/example_scripts directory</ulink>.</para> |
1049 |
</listitem> |
</listitem> |
1050 |
</varlistentry> |
</varlistentry> |
1051 |
|
|
1052 |
<varlistentry> |
<varlistentry> |
1053 |
<term><filename>-command='some command to run'</></term> |
<term><filename>-command='some command to run'</></term> |
1054 |
<listitem> |
<listitem> |
1055 |
<para>For some tests, particularly MPI runs, the default "make |
<para>For some tests, particularly MPI runs, a specific command |
1056 |
output.txt" is not sufficient. This option allows a more general |
might be needed to run the executable. This option allows a more general |
1057 |
command (or shell script) to be invoked. Examples of PBS scripts |
command (or shell script) to be invoked. Examples of PBS scripts |
1058 |
using MPI with testreport can be found in the <ulink |
using testreport with MPI can be found in the <ulink |
1059 |
url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/"> |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/"> |
1060 |
MITgcm-contrib area</ulink></para> |
tools/example_scripts directory</ulink>.</para> |
1061 |
|
<para> |
1062 |
|
For the case where the number of MPI processors varies according |
1063 |
|
to each test-experiment, some key-words within the command-to-run |
1064 |
|
argument will be replaced by their effective value:</para> |
1065 |
|
<para> |
1066 |
|
<filename>TR_NPROC </> will be replaced by the actual number |
1067 |
|
of MPI processors needed to run the current test-experiment.</para> |
1068 |
|
<para> |
1069 |
|
<filename>TR_MFILE </> will be replaced by the name of local-file |
1070 |
|
that testreport creates from the full list of machines which |
1071 |
|
"<filename>testreport -mf MACHINE_FILE</>" provides, but truncated |
1072 |
|
to the exact number of machines.</para> |
1073 |
|
</listitem> |
1074 |
|
</varlistentry> |
1075 |
|
|
1076 |
|
<varlistentry> |
1077 |
|
<term><filename>-mf MACHINE_FILE</></term> |
1078 |
|
<listitem> |
1079 |
|
<para> |
1080 |
|
To use with <filename>-MPI NUMBER_OF_PROCS</> option, to specify |
1081 |
|
the file containing the full list of <filename>NUMBER_OF_PROCS</> |
1082 |
|
machines to use for the MPI runs.</para> |
1083 |
|
</listitem> |
1084 |
|
</varlistentry> |
1085 |
|
|
1086 |
|
<varlistentry> |
1087 |
|
<term><filename>-mth</></term> |
1088 |
|
<listitem> |
1089 |
|
<para>compile (with <filename>genmake2 -omp</>) and run with |
1090 |
|
multiple threads (using eedata.mth).</para> |
1091 |
</listitem> |
</listitem> |
1092 |
</varlistentry> |
</varlistentry> |
1093 |
|
|
1094 |
</variablelist> |
</variablelist> |
1095 |
|
|
1096 |
<para>The <filename>testreport</> script will write progress to the |
<para>The <filename>testreport</> script will create an output directory |
1097 |
screen (stdout) as it runs. In addition, it will create a |
<filename>tr_NAME_DATE_N/ </>, with <filename>hostname</> as default |
1098 |
<filename>tr_out.txt</> file that contains a brief comparison of the |
<filename>NAME</>, <filename>DATE</> the current date followed by |
1099 |
current output with the "known-good" output.</para> |
a suffix number "N" to distinguish from previous |
1100 |
|
<filename>testreport</> output directories. |
1101 |
|
<filename>testreport</> writes progress to the screen (stdout) |
1102 |
|
and reports into the ouput directory as it runs. |
1103 |
|
In particular, one can find, in the ouput directory, |
1104 |
|
the <filename>summary.txt</> file that contains a brief comparison |
1105 |
|
of the current output with the "known-good" output. |
1106 |
|
At the end of the testing process, the <filename>tr_out.txt</> file |
1107 |
|
is generated in <filename>$ROOTDIR/verification/ </> |
1108 |
|
as a compact version of <filename>summry.txt</> file.</para> |
1109 |
|
|
1110 |
|
</sect3> |
1111 |
|
|
1112 |
|
<sect3 id="tst_2plus2"> |
1113 |
|
<title>The <filename>do_tst_2+2</> Utility</title> |
1114 |
|
<para> The shell script <filename>do_tst_2+2</> (in |
1115 |
|
<filename>$ROOTDIR/tools/ </>) |
1116 |
|
can be used to check the accuracy of the restart procedure. |
1117 |
|
</para> |
1118 |
</sect3> |
</sect3> |
1119 |
|
|
1120 |
</sect2> |
</sect2> |
1130 |
the generic fluid dynamical engine.</para> |
the generic fluid dynamical engine.</para> |
1131 |
|
|
1132 |
<para>The MITgcmUV packaging structure is described below using generic |
<para>The MITgcmUV packaging structure is described below using generic |
1133 |
package names ${pkg}. A concrete examples of a package is the code for |
package names ${pkg}. A concrete examples of a package is the code for |
1134 |
implementing GM/Redi mixing. This code uses the package name</para> |
implementing GM/Redi mixing. This code uses the package name</para> |
1135 |
|
|
1136 |
</sect2> |
</sect2> |
1155 |
below using generic package names ${pkg}. |
below using generic package names ${pkg}. |
1156 |
A concrete examples of a package is the code |
A concrete examples of a package is the code |
1157 |
for implementing GM/Redi mixing. This code uses |
for implementing GM/Redi mixing. This code uses |
1158 |
the package name |
the package name |
1159 |
* ${PKG} = GMREDI |
* ${PKG} = GMREDI |
1160 |
* ${pkg} = gmredi |
* ${pkg} = gmredi |
1161 |
* ${Pkg} = gmRedi |
* ${Pkg} = gmRedi |
1190 |
Package runtime config. options are imported |
Package runtime config. options are imported |
1191 |
into a common block held in a header file |
into a common block held in a header file |
1192 |
called "${PKG}.h". |
called "${PKG}.h". |
1193 |
|
Note: In some packages, the header file "${PKG}.h" is splitted |
1194 |
|
into "${PKG}_PARAMS.h" that contains the package parameters and |
1195 |
|
${PKG}_VARS.h" for the field arrays. |
1196 |
|
|
1197 |
o The core driver part of the model can check |
o The core driver part of the model can check |
1198 |
for runtime enabling or disabling of individual packages |
for runtime enabling or disabling of individual packages |
1215 |
1. Within the core driver code flags of the form |
1. Within the core driver code flags of the form |
1216 |
ALLOW_${PKG} are used to include or exclude |
ALLOW_${PKG} are used to include or exclude |
1217 |
whole packages. The ALLOW_${PKG} flags are included |
whole packages. The ALLOW_${PKG} flags are included |
1218 |
from a PKG_CPP_OPTIONS block which is currently |
from a PACKAGES_CONFIG.h file that is automatically |
1219 |
|
generated by genmake2 (see genmake2 section). |
1220 |
held in-line in the CPP_OPTIONS.h header file. |
held in-line in the CPP_OPTIONS.h header file. |
1221 |
e.g. |
e.g. |
1222 |
|
|
1223 |
Core model code ..... |
Core model code ..... |
1224 |
|
|
1225 |
|
#include "PACKAGES_CONFIG.h" |
1226 |
#include "CPP_OPTIONS.h" |
#include "CPP_OPTIONS.h" |
1227 |
: |
: |
1228 |
: |
: |
1234 |
|
|
1235 |
2. Within an individual package a header file, |
2. Within an individual package a header file, |
1236 |
"${PKG}_OPTIONS.h", is used to set CPP flags |
"${PKG}_OPTIONS.h", is used to set CPP flags |
1237 |
specific to that package. It is not recommended |
specific to that package. It also includes |
1238 |
to include this file in "CPP_OPTIONS.h". |
"PACKAGES_CONFIG.h" and "CPP_OPTIONS.h". |
1239 |
|
|
1240 |
|
|
1241 |
Package Boot Sequence |
Package Boot Sequence |
1248 |
1. S/R PACKAGES_BOOT() |
1. S/R PACKAGES_BOOT() |
1249 |
: |
: |
1250 |
CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... ) |
CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... ) |
1251 |
|
|
1252 |
|
|
1253 |
2. S/R PACKAGES_READPARMS() |
2. S/R PACKAGES_READPARMS() |
1254 |
: |
: |
1257 |
& CALL ${PKG}_READPARMS( retCode ) |
& CALL ${PKG}_READPARMS( retCode ) |
1258 |
#endif |
#endif |
1259 |
|
|
1260 |
2. S/R PACKAGES_CHECK() |
3. S/R PACKAGES_INIT_FIXED() |
1261 |
|
: |
1262 |
|
#ifdef ALLOW_${PKG} |
1263 |
|
if ( use${Pkg} ) |
1264 |
|
& CALL ${PKG}_INIT_FIXED( retCode ) |
1265 |
|
#endif |
1266 |
|
|
1267 |
|
4. S/R PACKAGES_CHECK() |
1268 |
: |
: |
1269 |
#ifdef ALLOW_${PKG} |
#ifdef ALLOW_${PKG} |
1270 |
if ( use${Pkg} ) |
if ( use${Pkg} ) |
1274 |
& CALL PACKAGES_CHECK_ERROR('${PKG}') |
& CALL PACKAGES_CHECK_ERROR('${PKG}') |
1275 |
#endif |
#endif |
1276 |
|
|
1277 |
3. S/R PACKAGES_INIT() |
5. S/R PACKAGES_INIT_VARIABLES() |
1278 |
: |
: |
1279 |
#ifdef ALLOW_${PKG} |
#ifdef ALLOW_${PKG} |
1280 |
if ( use${Pkg} ) |
if ( use${Pkg} ) |
1281 |
& CALL ${PKG}_INIT( retCode ) |
& CALL ${PKG}_INIT_VARIA( ) |
1282 |
|
#endif |
1283 |
|
|
1284 |
|
Package Output |
1285 |
|
============== |
1286 |
|
6. S/R DO_THE_MODEL_IO |
1287 |
|
|
1288 |
|
#ifdef ALLOW_${PKG} |
1289 |
|
if ( use${Pkg} ) |
1290 |
|
& CALL ${PKG}_OUTPUT( ) |
1291 |
#endif |
#endif |
1292 |
|
|
1293 |
|
7. S/R PACKAGES_WRITE_PICKUP() |
1294 |
|
|
1295 |
|
#ifdef ALLOW_${PKG} |
1296 |
|
if ( use${Pkg} ) |
1297 |
|
& CALL ${PKG}_WRITE_PICKUP( ) |
1298 |
|
#endif |
1299 |
|
|
1300 |
Description |
Description |
1301 |
=========== |
=========== |
1302 |
|
|
1303 |
- ${PKG}_READPARMS() |
- ${PKG}_READPARMS() |
1304 |
is responsible for reading |
is responsible for reading |
1305 |
in the package parameters file data.${pkg}, and storing |
in the package parameters file data.${pkg}, and storing |
1306 |
the package parameters in "${PKG}.h". |
the package parameters in "${PKG}.h" (or in "${PKG}_PARAMS.h"). |
1307 |
-> called in INITIALISE_FIXED |
-> called from INITIALISE_FIXED in PACKAGES_READPARMS |
1308 |
|
|
1309 |
|
- ${PKG}_INIT_FIXED() |
1310 |
|
is responsible for completing the internal setup of a package. |
1311 |
|
-> called from INITIALISE_FIXED in PACKAGES_INIT_FIXED |
1312 |
|
note: 1) some pkg use instead: |
1313 |
|
CALL ${PKG}_INITIALISE ( or the old form CALL ${PKG}_INIT ) |
1314 |
|
2) for simple pkg setup, this part is done inside ${PKG}_READPARMS |
1315 |
|
|
1316 |
- ${PKG}_CHECK() |
- ${PKG}_CHECK() |
1317 |
is responsible for validating |
is responsible for validating |
1318 |
basic package setup and inter-package dependencies. |
basic package setup and inter-package dependencies. |
1319 |
${PKG}_CHECK can import other package parameters it may |
${PKG}_CHECK can import other package parameters it may |
1320 |
need to check. This is done through header files "${PKG}.h". |
need to check. This is done through header files "${PKG}.h". |
1321 |
It is assumed that parameters owned by other packages |
It is assumed that parameters owned by other packages |
1322 |
will not be reset during ${PKG}_CHECK(). |
will not be reset during ${PKG}_CHECK(). |
1323 |
-> called in INITIALISE_FIXED |
-> called from INITIALISE_FIXED in PACKAGES_CHECK |
1324 |
|
|
1325 |
- ${PKG}_INIT() |
- ${PKG}_INIT_VARIA() |
1326 |
is responsible for completing the |
is responsible for fill-in all package variables with an initial value. |
1327 |
internal setup of a package. This routine is called after |
Contains eventually a call to ${PKG}_READ_PICKUP that will read |
1328 |
the core model state has been completely initialised |
from a pickup file the package variables required to restart the model. |
1329 |
but before the core model timestepping starts. |
This routine is called after the core model state has been completely |
1330 |
-> called in INITIALISE_VARIA |
initialised but before the core model timestepping starts. |
1331 |
|
-> called from INITIALISE_VARIA in PACKAGES_INIT_VARIABLES |
1332 |
|
note: the name ${PKG}_INIT_VARIA is not yet standard and some pkg |
1333 |
|
use for e.g. ${PKG}_INI_VARS, ${PKG}_INIT_VARIABLES, or the old |
1334 |
|
form ${PKG}_INIT |
1335 |
|
|
1336 |
|
- ${PKG}_OUTPUT( ) |
1337 |
|
is responsible for writing time-average fields to output files |
1338 |
|
(but the cumulating step is done within the package main S/R). |
1339 |
|
Can also contain other diagnostics (.e.g. CALL ${PKG}_MONITOR) |
1340 |
|
and write snap-shot fields that are hold in common blocks. Other |
1341 |
|
temporary fields are directly dump to file where they are available. |
1342 |
|
NOTE: 1) the S/R old name ${PKG}_DIAGS is used in some packages |
1343 |
|
but is beeing replaced by ${PKG}_OUTPUT |
1344 |
|
to avoid confusion with pkg/diagnostics functionality. |
1345 |
|
2) the output part is not yet in a standard form and might still |
1346 |
|
evolve a lot. |
1347 |
|
-> called within DO_THE_MODEL_IO |
1348 |
|
|
1349 |
|
- ${PKG}_WRITE_PICKUP() |
1350 |
|
is responsible for writing a package pickup file when necessary for |
1351 |
|
a restart. (found also the old name: ${PKG}_WRITE_CHECKPOINT ) |
1352 |
|
-> called from FORWARD_STEP and THE_MODEL_MAIN in PACKAGES_WRITE_PICKUP |
1353 |
|
|
1354 |
Summary |
Summary |
1355 |
======= |
======= |
1370 |
----------------------- |
----------------------- |
1371 |
* ${PKG}_OPTIONS.h has further package-specific CPP options |
* ${PKG}_OPTIONS.h has further package-specific CPP options |
1372 |
* ${PKG}.h package-specific common block variables, fields |
* ${PKG}.h package-specific common block variables, fields |
1373 |
|
or ${PKG}_PARAMS.h package-specific common block parameters |
1374 |
|
and ${PKG}_VARS.h package-specific common block fields |
1375 |
|
|
1376 |
- FORTRAN source files |
- FORTRAN source files |
1377 |
----------------------- |
----------------------- |
1378 |
* ${pkg}_readparms.F reads parameters from file data.${pkg} |
* ${pkg}_readparms.F reads parameters from file data.${pkg} |
1379 |
* ${pkg}_check.F checks package dependencies and consistencies |
* ${pkg}_init_fixed.F complete the package setup |
1380 |
* ${pkg}_init.F initialises package-related fields |
* ${pkg}_check.F checks package dependencies and consistencies |
1381 |
* ${pkg}_... .F package source code |
* ${pkg}_init_varia.F initialises package-related fields |
1382 |
|
* ${pkg}_... .F package source code |
1383 |
|
* ${pkg}_output.F write output to file. |
1384 |
|
* ${pkg}_write_pickup.F write a package pickup file to restart the model |
1385 |
|
|
1386 |
|
New: Subroutine in one package (pkgA) that only contains code which |
1387 |
|
is connected to a 2nd package (pkgB) (e.g.: gmredi_diagnostics_init.F) |
1388 |
|
will be named: pkgA_pkgB_something.F |
1389 |
|
|
1390 |
- parameter file |
- parameter file |
1391 |
----------------------- |
----------------------- |
1395 |
</sect1> |
</sect1> |
1396 |
|
|
1397 |
|
|
1398 |
|
<sect1 id="documentation"> |
1399 |
|
<title>Editing the Documentation</title> |
1400 |
|
|
1401 |
|
<sect2 id="documentation_getting"> |
1402 |
|
<title>Getting the Docs and Code</title> |
1403 |
|
|
1404 |
|
<para>The first step towards editing the documentation is to checkout a |
1405 |
|
copy of code, docs, and build scripts from the CVS server using:</para> |
1406 |
|
|
1407 |
|
<screen> |
1408 |
|
$ export CVS_RSH=ssh |
1409 |
|
$ export CVSROOT=':ext:NAME@mitgcm.org:/u/gcmpack' |
1410 |
|
$ mkdir scratch |
1411 |
|
$ cvs co -P MITgcm manual mitgcm.org |
1412 |
|
</screen> |
1413 |
|
|
1414 |
|
<para>These commands extract the necessary information from the CVS server |
1415 |
|
and create a temporary (called <filename>scratch</filename>) directory for |
1416 |
|
the storage of the HTML and other files that will be created. Please note |
1417 |
|
that you must either create <filename>scratch</filename> as shown or edit |
1418 |
|
the various <filename>Makefile</filename>s and scripts used to create the |
1419 |
|
documentation.</para> |
1420 |
|
</sect2> |
1421 |
|
|
1422 |
|
<sect2> |
1423 |
|
<title>Editing the Documentation</title> |
1424 |
|
|
1425 |
|
<para>The documentation is contained in the <filename>manual</filename> |
1426 |
|
directory in a raw LaTeX format. The main document is |
1427 |
|
<filename>manual.tex</filename> and it uses <command>\input{}</command>s |
1428 |
|
to include the chapters and subsections.</para> |
1429 |
|
|
1430 |
|
<para>Since the same LaTeX source is used to produce PostScript, PDF, and |
1431 |
|
HTML output, care should be taken to follow certain conventions. Two of |
1432 |
|
the most important are the usage of the <command>\filelink{}{}</command> |
1433 |
|
and <command>\varlink{}{}</command> commands. Both of these commands have |
1434 |
|
been defined to simplify the connection between the automatically |
1435 |
|
generated ("code browser") HTML and the HTML version of the manual |
1436 |
|
produced by LaTeX2HTML. They each take two arguments (corresponding to |
1437 |
|
the contents of the two sets of curly braces) which are the text that the |
1438 |
|
author wishes to be "wrapped" within the link, and a specially formatted |
1439 |
|
link thats relative to the <filename>MITgcm</filename> directory within |
1440 |
|
the CVS tree.</para> |
1441 |
|
|
1442 |
|
<para>The result is a command that resembles either</para> |
1443 |
|
|
1444 |
|
<orderedlist> |
1445 |
|
<listitem> |
1446 |
|
<para>a reference to a variable or subroutine name such as |
1447 |
|
<command>\varlink{tRef}{tRef}</command>, or </para> |
1448 |
|
</listitem> |
1449 |
|
|
1450 |
|
<listitem> |
1451 |
|
<para>a reference to a file such as |
1452 |
|
<command>\varlink{tRef}{path-to-the-file_name.F}</command> |
1453 |
|
where the absolute path to the file is of the form |
1454 |
|
<filename>/foo/MITgcm/path/to/the/file_name.F</filename></para> |
1455 |
|
<para>(please note how the leading "/foo/MITgcm" |
1456 |
|
component of the path is dropped leaving the path |
1457 |
|
<emphasis>relative</emphasis> to the head of the code |
1458 |
|
directory and each directory separator "/" is turned |
1459 |
|
into a "-")</para> |
1460 |
|
</listitem> |
1461 |
|
</orderedlist> |
1462 |
|
|
1463 |
|
|
1464 |
|
|
1465 |
|
</sect2> |
1466 |
|
|
1467 |
|
<sect2> |
1468 |
|
<title>Building the Documentation</title> |
1469 |
|
|
1470 |
|
<para>Given the directory structure of <xref |
1471 |
|
linkend="documentation_getting">, the entire documentation for the web |
1472 |
|
site can be built using:</para> |
1473 |
|
|
1474 |
|
<screen> |
1475 |
|
$ cd mitgcm.org/devel/buildweb |
1476 |
|
$ make All |
1477 |
|
</screen> |
1478 |
|
|
1479 |
|
<para>Which builds the PDF from the LaTeX source, creates the HTML output |
1480 |
|
from the LaTeX source, parses the FORTRAN code base to produce a |
1481 |
|
hyperlinked HTML version of the source, and then determines the |
1482 |
|
cross-linking between the various HTML components.</para> |
1483 |
|
|
1484 |
|
<para>If there are no errors, the result of the build process (which can |
1485 |
|
take 30+ minutes on a P4/2.5Ghz) will be contained within a single |
1486 |
|
directory called <filename>scratch/dev_docs</filename>. This is a freshly |
1487 |
|
built version of the entire on-line users manual. If you have the correct |
1488 |
|
permissions, it can be directly copied to the web server area:</para> |
1489 |
|
|
1490 |
|
<screen> |
1491 |
|
$ mv scratch/dev_docs /u/u0/httpd/html |
1492 |
|
</screen> |
1493 |
|
|
1494 |
|
<para>and the update is complete.</para> |
1495 |
|
|
1496 |
|
</sect2> |
1497 |
|
|
1498 |
|
</sect1> |
1499 |
|
|
1500 |
</article> |
</article> |
1501 |
|
|
1502 |
|
|