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<article id="MITgcm-Development-HOWTO"> |
<article id="MITgcm-Development-HOWTO"> |
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db2pdf -d ldp.dsl devel_HOWTO.sgml |
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<articleinfo> |
<articleinfo> |
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<title>MITgcm Development HOWTO</title> |
<title>MITgcm Development HOWTO</title> |
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|
| 16 |
<revhistory> |
<revhistory> |
| 17 |
<revision> |
<revision> |
| 18 |
<revnumber>0.01</revnumber> |
<revnumber>0.01</revnumber> |
| 19 |
<date>2003-0-07</date> |
<date>2003-08-07</date> |
| 20 |
<authorinitials>eh3</authorinitials> |
<authorinitials>eh3</authorinitials> |
| 21 |
<revremark> |
<revremark> |
| 22 |
Initial version. |
Initial version. |
| 23 |
</revremark> |
</revremark> |
| 24 |
</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> |
| 29 |
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<revremark> |
| 30 |
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update links. |
| 31 |
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</revremark> |
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</revision> |
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<revision> |
| 34 |
|
<revnumber>0.03</revnumber> |
| 35 |
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<date>2010-04-25</date> |
| 36 |
|
<authorinitials>jmc</authorinitials> |
| 37 |
|
<revremark> |
| 38 |
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Add subsection "Developer settings" (under CVS Repository). |
| 39 |
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</revremark> |
| 40 |
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</revision> |
| 41 |
</revhistory> |
</revhistory> |
| 42 |
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|
| 43 |
<abstract> |
<abstract> |
| 53 |
<sect2> |
<sect2> |
| 54 |
<title>New Versions of This Document</title> <para>You can |
<title>New Versions of This Document</title> <para>You can |
| 55 |
obtain the latest version of this document <ulink |
obtain the latest version of this document <ulink |
| 56 |
url="http://mitgcm.org/dev_docs/devel_HOWTO/">online</ulink> in |
url="http://mitgcm.org/public/docs.html">online</ulink> in |
| 57 |
various formats.</para> |
various formats.</para> |
| 58 |
</sect2> |
</sect2> |
| 59 |
<sect2> |
<sect2> |
| 71 |
<sect2> |
<sect2> |
| 72 |
<title>User Manual</title> |
<title>User Manual</title> |
| 73 |
|
|
| 74 |
<para>Before jumping into |
<para>Before jumping into development, please familiarize yourself with |
| 75 |
development, please familiarize yourself with the MITgcm user |
the <ulink url="http://mitgcm.org/public/docs.html"> MITgcm user manual |
| 76 |
manual which is available <ulink |
</ulink>. This document contains volumes of useful information and is |
| 77 |
url="http://mitgcm.org/">on the main web page</ulink>. This |
included here by reference.</para> |
|
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 |
| 81 |
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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|
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<sect2> |
<sect2> |
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<title>Layout</title> |
<title>Layout</title> |
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|
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others. The tree currently resembles:</para> |
others. The tree currently resembles:</para> |
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|
|
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<programlisting>gcmpack/ |
<programlisting>gcmpack/ |
|
MITgcm-contrib contributed code |
|
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CS-regrid goes into utils |
CS-regrid goes into utils |
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cvspolicy.html -save- |
CVSROOT -hidden- |
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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) |
| 131 |
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) |
| 136 |
| 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 |
| 148 |
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gcmpack an old back-up copy ? |
| 149 |
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gfd_lab -?- |
| 150 |
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manual -save- |
| 151 |
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misc -?- |
| 152 |
mitgcm.org build web site |
mitgcm.org build web site |
| 153 |
|
mitgcmdoc -> manual -remove- |
| 154 |
models -?- |
models -?- |
| 155 |
packages -?- |
packages -?- |
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pdfs some pdfs |
| 157 |
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planetinabottle.org unfinished web site |
| 158 |
preprocess -?- |
preprocess -?- |
| 159 |
tmp -?- |
tmp -?- |
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www.ecco-group.org build ecco web site ? |
| 161 |
</programlisting> |
</programlisting> |
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<!-- |
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<para>Efforts are underway to reduce the complexity.</para> |
<para>Efforts are underway to reduce the complexity.</para> |
| 165 |
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--> |
| 166 |
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| 167 |
</sect2> |
</sect2> |
| 168 |
|
|
| 201 |
<title>Branches</title> |
<title>Branches</title> |
| 202 |
|
|
| 203 |
<para>As shown in the online <ulink |
<para>As shown in the online <ulink |
| 204 |
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"> |
| 205 |
tree</ulink>, the MITgcm codebase is split into to two branches |
ViewCVS-generated tree</ulink>, the MITgcm codebase is split into to two |
| 206 |
or "lines" under which development proceeds. These two lines |
branches or "lines" under which development proceeds. These two lines are |
| 207 |
are referred to as the "MAIN" and "ecco" versions of the code. |
referred to as the "MAIN" and "ecco" versions of the code. While not |
| 208 |
While not identical, the bulk of the MAIN and ecco lines are |
identical, the bulk of the MAIN and ecco lines are composed of files from |
| 209 |
composed of files from the same codebase. |
the same codebase. |
| 210 |
</para> |
</para> |
| 211 |
|
|
| 212 |
<para>Periodically, a "Release" branch is formed from the "MAIN" |
<para>Periodically, a "Release" branch is formed from the "MAIN" |
| 213 |
development branch. This is done in order to create a |
development branch. This is done in order to create a relatively stable |
| 214 |
relatively stable reference point for both users and developers. |
reference point for both users and developers. The intent is that once a |
| 215 |
The intent is that once a relese branch has been created, only |
relese branch has been created, only bug-fixes will be added to it. |
| 216 |
bug-fixes will be added to it. Meanwhile, development (which |
Meanwhile, development (which might "break" or otherwise render invalid |
| 217 |
might "break" or otherwise render invalid the documentation, |
the documentation, tutorials, and/or examples contained within a release |
| 218 |
tutorials, and/or examples contained within a release branch) is |
branch) is allowed to continue along the MAIN and ecco lines.</para> |
| 219 |
allowed to continue along the MAIN and ecco lines.</para> |
</sect2> |
| 220 |
|
|
| 221 |
|
<sect2> |
| 222 |
|
<title> Developer settings </title> |
| 223 |
|
|
| 224 |
|
<para>CVS is a convenient tool to keep up-to-date a personal copy of the |
| 225 |
|
MITgcm code (see: <ulink url="http://mitgcm.org/public/using_cvs.html"> |
| 226 |
|
using CVS </ulink>). The same tool is used by developers to |
| 227 |
|
incorporate any change into the repository. However, this later |
| 228 |
|
function requires specific settings, as detailed here after:</para> |
| 229 |
|
<orderedlist> |
| 230 |
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<listitem> |
| 231 |
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<para> You will need an account (loggin access) to the server |
| 232 |
|
"mitgcm.org" with the proper group setting (e.g., |
| 233 |
|
group "gcmctrb" to add/modify code into MITgcm_contrib). |
| 234 |
|
This kind of account is granted only upon well motivated request. |
| 235 |
|
The access to the server mitgcm.org is through ssh-key authorization |
| 236 |
|
which will need to be set properly on both side (on your local machine |
| 237 |
|
and on your server account). You need to be able to |
| 238 |
|
to ssh to mitgcm.org (or <filename>ssh MY_USER_NAME@mitgcm.org</filename> |
| 239 |
|
in case of different user-name on both sides) to proceed further.</para> |
| 240 |
|
</listitem> |
| 241 |
|
|
| 242 |
|
<listitem> |
| 243 |
|
<para> You need to register to the |
| 244 |
|
<ulink url="http://mitgcm.org/mailman/listinfo/mitgcm-cvs"> |
| 245 |
|
mitgcm-cvs </ulink> mailing list. |
| 246 |
|
This ensures that other developers will receive email notification |
| 247 |
|
when you make changes; you will also receive as well such email |
| 248 |
|
when others make changes to the repository. |
| 249 |
|
</para> |
| 250 |
|
</listitem> |
| 251 |
|
|
| 252 |
|
<listitem> |
| 253 |
|
<para> It is highly recommended that you register also to the |
| 254 |
|
<ulink url="http://mitgcm.org/mailman/listinfo/mitgcm-devel"> |
| 255 |
|
mitgcm-devel </ulink> mailing list (expect a short delay for |
| 256 |
|
this request to be processed). |
| 257 |
|
This list is intended for developer discussions. |
| 258 |
|
</para> |
| 259 |
|
</listitem> |
| 260 |
|
|
| 261 |
|
<listitem> |
| 262 |
|
<para> The standard anonymous mode (using "cvsanon", as mentionned |
| 263 |
|
<ulink url="http://mitgcm.org/public/source_code.html"> |
| 264 |
|
here </ulink>) does not allow check-in ("cvs commit") permission. |
| 265 |
|
Instead, you will need to set our CVS environment as follow:</para> |
| 266 |
|
<screen> |
| 267 |
|
$ export CVS_RSH=ssh |
| 268 |
|
$ export CVSROOT=':ext:MY_USER_NAME@mitgcm.org:/u/gcmpack' |
| 269 |
|
</screen> |
| 270 |
|
<para> After downloading a directory, e.g.: <filename>myCopy</filename>, |
| 271 |
|
from the CVS repository (e.g., |
| 272 |
|
<filename>MITgcm_contrib/thisPart</filename>) using the command:</para> |
| 273 |
|
<screen> |
| 274 |
|
$ cvs co -P -d myCopy MITgcm_contrib/thisPart |
| 275 |
|
</screen> |
| 276 |
|
<para> the type of CVS environment which has been used |
| 277 |
|
is stored in the file <filename>myCopy/CVS/Root</filename> |
| 278 |
|
and makes it difficult to re-use, for cvs-commit purpose, |
| 279 |
|
a cvs local copy (<filename>myCopy</filename>) which was obtained |
| 280 |
|
using the CVS anonymous mode.</para> |
| 281 |
|
</listitem> |
| 282 |
|
|
| 283 |
|
<listitem> |
| 284 |
|
<para> At this stage, you should be able to send your modified source |
| 285 |
|
file (e.g., <filename>src_file</filename>) from your local copy directory |
| 286 |
|
(<filename>myCopy</filename>) to the CVS repository |
| 287 |
|
(<filename>MITgcm_contrib/thisPart</filename>) using the command |
| 288 |
|
"cvs commit":</para> |
| 289 |
|
<screen> |
| 290 |
|
$ cd myCopy |
| 291 |
|
$ cvs -n update (optional; check if new changes have been made) |
| 292 |
|
$ cvs diff src_file (optional; list your changes) |
| 293 |
|
$ cvs commit src_file |
| 294 |
|
</screen> |
| 295 |
|
<para> It is essential that you provide a short description of the |
| 296 |
|
changes you made to <filename>src_file</filename> as you check-in |
| 297 |
|
this file (the "cvs commit" command automatically opens your standard |
| 298 |
|
editor for this purpose).</para> |
| 299 |
|
</listitem> |
| 300 |
|
|
| 301 |
|
</orderedlist> |
| 302 |
|
|
| 303 |
</sect2> |
</sect2> |
| 304 |
|
|
| 305 |
<sect2> |
<sect2> |
| 306 |
<title>Tagging</title> |
<title>Main code development</title> |
| 307 |
|
<para>(formerly named "Tagging" ; this section needs an update)</para> |
| 308 |
<para>The intent of tagging is to create "known-good" |
|
| 309 |
checkpoints that developers can use as references. |
<para>The intent of tagging is to create "known-good" checkpoints that |
| 310 |
Traditionally, MITgcm tagging has maintained the following |
developers can use as references. Traditionally, MITgcm tagging has |
| 311 |
conventions:</para> |
maintained the following conventions:</para> |
| 312 |
|
|
| 313 |
<orderedlist> |
<orderedlist> |
| 314 |
<listitem> |
<listitem> |
| 315 |
<para>Developer checks out code into a local CVS-managed |
<para>Developer checks out code into a local CVS-managed directory, |
| 316 |
directory, makes various changes/additions, tests these |
makes various changes/additions, tests these edits, and eventually |
| 317 |
edits, and eventually reaches a point where (s)he is |
reaches a point where (s)he is satisfied that the changes form a new |
| 318 |
satisfied that the changes form a new "useful" point in the |
"useful" point in the evolution of the code.</para> |
|
evolution of the code.</para> |
|
| 319 |
</listitem> |
</listitem> |
| 320 |
|
|
| 321 |
<listitem> |
<listitem> |
| 322 |
<para>The developer then runs the <ulink |
<para>The developer then runs the <ulink |
| 323 |
url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/verification/testscript">testscript</ulink> |
url="http://mitgcm.org/viewvc/MITgcm/MITgcm/verification/testreport"> |
| 324 |
shell script to see if any problems are introduced. While |
testreport</ulink> shell script to see if any problems are introduced. |
| 325 |
not intended to be exhaustive, the test cases within the |
While not intended to be exhaustive, the test cases within the |
| 326 |
verification directory do provide some indication whether |
verification directory do provide some indication whether gross errors |
| 327 |
gross errors have been introduced. |
have been introduced. |
| 328 |
</para> |
</para> |
| 329 |
</listitem> |
</listitem> |
| 330 |
|
|
| 334 |
then:</para> |
then:</para> |
| 335 |
<orderedlist> |
<orderedlist> |
| 336 |
<listitem> |
<listitem> |
| 337 |
<para>adds a "checkpointXY_pre" comment (where X is a |
<para>adds a "checkpointXY_pre" comment (where X is a checkpoint |
| 338 |
checkpoint number and Y is a letter) to the <ulink |
number and Y is a letter) to the <ulink |
| 339 |
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"> |
| 340 |
file and checks it into the CVS repository</para> |
tag-index</ulink> file and checks it into the CVS |
| 341 |
|
repository</para> |
| 342 |
</listitem> |
</listitem> |
| 343 |
<listitem> |
<listitem> |
| 344 |
<para>submits the set of changes to the CVS repository |
<para>submits the set of changes to the CVS repository and adds |
| 345 |
and adds comments to <filename>tag-index</filename> |
comments to <filename>tag-index</filename> describing what the |
| 346 |
describing what the changes are along with a matching |
changes are along with a matching "checkpointXY_post" entry</para> |
|
"checkpointXY_post" entry</para> |
|
| 347 |
</listitem> |
</listitem> |
| 348 |
</orderedlist> |
</orderedlist> |
| 349 |
</listitem> |
</listitem> |
| 350 |
</orderedlist> |
</orderedlist> |
| 351 |
|
|
| 352 |
<para>The result of this tagging procedure is a sequence of |
<para>The result of this tagging procedure is a sequence of development |
| 353 |
development checkpoints with comments which resembles:</para> |
checkpoints with comments which resembles:</para> |
| 354 |
|
|
| 355 |
<programlisting> |
<programlisting> |
| 356 |
checkpoint50e_post |
checkpoint50e_post |
| 372 |
checkpoint50d_pre |
checkpoint50d_pre |
| 373 |
</programlisting> |
</programlisting> |
| 374 |
|
|
| 375 |
<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 |
| 376 |
the code development. For example, bugs can be traced to |
development. For example, bugs can be traced to individual sets of CVS |
| 377 |
individual sets of CVS checkins based upon their first |
checkins based upon their first appearance when comparing the results from |
| 378 |
appearance when comparing the results from different |
different checkpoints.</para> |
|
checkpoints.</para> |
|
| 379 |
|
|
| 380 |
</sect2> |
</sect2> |
| 381 |
</sect1> |
</sect1> |
| 382 |
|
|
| 383 |
|
|
| 384 |
|
<sect1 id="coding"> |
| 385 |
|
<title>Coding for MITgcm</title> |
| 386 |
|
|
| 387 |
|
<sect2 id="build_tools"> |
| 388 |
|
<title>Build Tools</title> |
| 389 |
|
|
| 390 |
|
<para>Many Open Source projects use the "GNU Autotools" to help streamline |
| 391 |
|
the build process for various Unix and Unix-like architectures. For a |
| 392 |
|
user, the result is the common "configure" (that is, |
| 393 |
|
"<filename>./configure && make && make install</filename>") commands. |
| 394 |
|
For MITgcm, the process is similar. Typical commands are:</para> |
| 395 |
|
|
| 396 |
|
<screen> |
| 397 |
|
$ genmake -mods=../code |
| 398 |
|
$ make depend |
| 399 |
|
$ make |
| 400 |
|
</screen> |
| 401 |
|
|
| 402 |
|
<para>The following sections describe the individual steps in the build |
| 403 |
|
process.</para> |
| 404 |
|
|
| 405 |
|
<sect3 id="genmake"> |
| 406 |
|
<title>The <filename>genmake2</> Utility</title> |
| 407 |
|
|
| 408 |
|
<para><emphasis>Please note that the older <filename>genmake</> is |
| 409 |
|
deprecated and will eventually be replaced by <filename>genmake2</>. |
| 410 |
|
This HOWTO only describes the newer tool.</emphasis></para> |
| 411 |
|
|
| 412 |
|
<para>The first step in any MITgcm build is to create a Unix-style |
| 413 |
|
<filename>Makefile</filename> which will be parsed by |
| 414 |
|
<filename>make</filename> to specify how to compile the MITgcm source |
| 415 |
|
files. For more detailed descriptions of what the make tools are and |
| 416 |
|
how they are used, please see:</para> |
| 417 |
|
|
| 418 |
|
<itemizedlist> |
| 419 |
|
<listitem> |
| 420 |
|
<para><ulink url="http://www.gnu.org/software/make/make.html"> |
| 421 |
|
http://www.gnu.org/software/make/make.html</></para> |
| 422 |
|
</listitem> |
| 423 |
|
<listitem> |
| 424 |
|
<para><ulink url="http://www.oreilly.com/catalog/make2/"> |
| 425 |
|
http://www.oreilly.com/catalog/make2/</></para> |
| 426 |
|
</listitem> |
| 427 |
|
</itemizedlist> |
| 428 |
|
|
| 429 |
|
<para>Genmake can often be invoked successfully with a command line as |
| 430 |
|
simple as:</para> |
| 431 |
|
|
| 432 |
|
<screen> |
| 433 |
|
$ genmake2 -mods=../code |
| 434 |
|
</screen> |
| 435 |
|
|
| 436 |
|
<para>However, some systems (particularly commercial Unixes that lack a |
| 437 |
|
more modern "/bin/sh" implementation or that have shells installed in |
| 438 |
|
odd locations) may require an explicit shell invocation such as one of |
| 439 |
|
the following: </para> |
| 440 |
|
|
| 441 |
|
<screen> |
| 442 |
|
$ /usr/bin/sh genmake2 -make=gmake -mods=../code |
| 443 |
|
$ /opt/gnu/bin/bash genmake2 -ieee -make=/usr/local/bin/gmake -mods=../code |
| 444 |
|
</screen> |
| 445 |
|
|
| 446 |
|
<para>The genmake2 code has been written in a Bourne and BASH (v1) |
| 447 |
|
compatible syntax so it should work with most "sh" and all recent "bash" |
| 448 |
|
implementations.</para> |
| 449 |
|
|
| 450 |
|
<para>As the name implies, <filename>genmake2</filename> generates a |
| 451 |
|
<filename>Makefile</filename>. It does so by first parsing the |
| 452 |
|
information supplied from the following sources</para> |
| 453 |
|
|
| 454 |
|
<orderedlist> |
| 455 |
|
<listitem> |
| 456 |
|
<para>a <filename>gemake_local</filename> file in the current |
| 457 |
|
directory</para> |
| 458 |
|
</listitem> |
| 459 |
|
<listitem> |
| 460 |
|
<para>directly from command-line options</para> |
| 461 |
|
</listitem> |
| 462 |
|
<listitem> |
| 463 |
|
<para>an "options file" as specified by the command-line option |
| 464 |
|
<filename>-optfile='FILENAME'</filename></para> |
| 465 |
|
</listitem> |
| 466 |
|
</orderedlist> |
| 467 |
|
|
| 468 |
|
<para>then checking certain dependency rules (the package dependencies), |
| 469 |
|
and finally writing a <filename>Makefile</filename> based upon the |
| 470 |
|
source code that it finds. For convenience within various Unix |
| 471 |
|
shells, <filename>genmake2</> supports both "long"- and "short"-style |
| 472 |
|
options. A complete list of the available options can be obtained |
| 473 |
|
from:</para> |
| 474 |
|
|
| 475 |
|
<screen> |
| 476 |
|
$ genmake2 -help |
| 477 |
|
</screen> |
| 478 |
|
|
| 479 |
|
<para>The most important options for <filename>genmake2</> are:</para> |
| 480 |
|
|
| 481 |
|
<variablelist> |
| 482 |
|
|
| 483 |
|
<varlistentry> |
| 484 |
|
<term><filename>--optfile=/PATH/FILENAME</></term> |
| 485 |
|
|
| 486 |
|
<listitem> |
| 487 |
|
<para>This specifies the "options file" that should be used for a |
| 488 |
|
particular build. The options file is a convenient and |
| 489 |
|
machine-indepenent way of specifying parameters such as the |
| 490 |
|
FORTRAN compiler (<filename>FC=</>), FORTRAN compiler |
| 491 |
|
optimization flags (<filename>FFLAGS=</>), and the locations of |
| 492 |
|
various platform- and/or machine-specific tools |
| 493 |
|
(eg. <filename>MAKEDEPEND=</>). As with <filename>genmake2</>, |
| 494 |
|
all options files should be written to be compatible with |
| 495 |
|
Bourne--shell ("sh" or "BASH v1") syntax. Examples of various |
| 496 |
|
options files can be found in |
| 497 |
|
<filename>$ROOTDIR/tools/build_options</>.</para> |
| 498 |
|
|
| 499 |
|
<para>If no "optfile" is specified (either through the command lin |
| 500 |
|
or the environment variable), genmake2 will try to make a |
| 501 |
|
reasonable guess from the list provided in |
| 502 |
|
<filename>$ROOTDIR/tools/build_options</>. The method used for |
| 503 |
|
making this guess is to first determine the combination of |
| 504 |
|
operating system and hardware (eg. "linux_ia32") and then find a |
| 505 |
|
working Fortran compiler within the user's path. When these |
| 506 |
|
three items have been identified, genmake2 will try to find an |
| 507 |
|
optfile that has a matching name. </para> |
| 508 |
|
|
| 509 |
|
<para>Everyone is encouraged to submit their options files to the |
| 510 |
|
MITgcm project for inclusion (please send to |
| 511 |
|
<email>MITgcm-support@mitgcm.org</email>). We are particularly |
| 512 |
|
grateful for options files tested on new or unique |
| 513 |
|
platforms!</para> |
| 514 |
|
</listitem> |
| 515 |
|
|
| 516 |
|
</varlistentry> |
| 517 |
|
|
| 518 |
|
<varlistentry> |
| 519 |
|
<term><filename>-pdepend=/PATH/FILENAME</></term> |
| 520 |
|
|
| 521 |
|
<listitem> |
| 522 |
|
<para>This specifies the dependency file used for packages. If |
| 523 |
|
not specified, the default dependency file is |
| 524 |
|
<filename>$ROOTDIR/pkg/pkg_depend</>. The syntax for this file is |
| 525 |
|
parsed on a line-by-line basis where each line containes either a |
| 526 |
|
comment ("#") or a simple "PKGNAME1 (+|-)PKGNAME2" pairwise rule |
| 527 |
|
where the "+" or "-" symbol specifies a "must be used with" or a |
| 528 |
|
"must not be used with" relationship, respectively. If no rule is |
| 529 |
|
specified, then it is assumed that the two packages are compatible |
| 530 |
|
and will function either with or without each other.</para> |
| 531 |
|
</listitem> |
| 532 |
|
</varlistentry> |
| 533 |
|
|
| 534 |
|
<varlistentry> |
| 535 |
|
<term><filename>-pdefault=PKG</></term> |
| 536 |
|
<term><filename>-pdefault='PKG1 [PKG2 PKG3 ...]'</></term> |
| 537 |
|
<listitem> |
| 538 |
|
<para>This option specifies the default set of packages |
| 539 |
|
to be used. If not set, the default package list will |
| 540 |
|
be read from |
| 541 |
|
<filename>$ROOTDIR/pkg/pkg_default</>.</para> |
| 542 |
|
</listitem> |
| 543 |
|
</varlistentry> |
| 544 |
|
|
| 545 |
|
<varlistentry> |
| 546 |
|
<term><filename>-adof=/path/to/file</></term> |
| 547 |
|
<term><filename>-adoptfile=/path/to/file</></term> |
| 548 |
|
<listitem> |
| 549 |
|
<para>This option specifies the "adjoint" or automatic |
| 550 |
|
differentiation options file to be used. The file is analogous |
| 551 |
|
to the "optfile" defined above but it specifies information for |
| 552 |
|
the AD build process. The default file is located in <filename> |
| 553 |
|
$ROOTDIR/tools/adjoint_options/adjoint_default </> and it |
| 554 |
|
defines the "TAF" and "TAMC" compilers. An alternate version is |
| 555 |
|
also available at <filename> |
| 556 |
|
$ROOTDIR/tools/adjoint_options/adjoint_staf </> that selects the |
| 557 |
|
newer "STAF" compiler. As with any compilers, it is helpful to |
| 558 |
|
have their directories listed in your $PATH environment |
| 559 |
|
variable.</para> |
| 560 |
|
</listitem> |
| 561 |
|
</varlistentry> |
| 562 |
|
|
| 563 |
|
<varlistentry> |
| 564 |
|
<term><filename>-mods=DIR</></term> |
| 565 |
|
<term><filename>-mods='DIR1 [DIR2 ...]'</></term> |
| 566 |
|
<listitem> |
| 567 |
|
<para>This option specifies a list of directories containing |
| 568 |
|
"modifications". These directories contain files with names |
| 569 |
|
that may (or may not) exist in the main MITgcm source tree but |
| 570 |
|
will be overridden by any identically-named sources within the |
| 571 |
|
"MODS" directories. The order of precedence for this |
| 572 |
|
"name-hiding" is as follows:</para> |
| 573 |
|
|
| 574 |
|
<itemizedlist> |
| 575 |
|
<listitem><para>"MODS" directories (in the order given) |
| 576 |
|
</para></listitem> |
| 577 |
|
<listitem><para>Packages either explicitly specified or |
| 578 |
|
provided by default (in the order given)</para></listitem> |
| 579 |
|
<listitem><para>Packages included due to package dependencies |
| 580 |
|
(in the order that that package dependencies are |
| 581 |
|
parsed)</para></listitem> |
| 582 |
|
<listitem><para>The "standard dirs" (which may have been |
| 583 |
|
specified by the "-standarddirs" option)</para></listitem> |
| 584 |
|
</itemizedlist> |
| 585 |
|
|
| 586 |
|
</listitem> |
| 587 |
|
</varlistentry> |
| 588 |
|
|
| 589 |
|
<varlistentry> |
| 590 |
|
<term><filename>-make=/path/to/gmake</></term> |
| 591 |
|
<listitem> |
| 592 |
|
<para>Due to the poor handling of soft-links and other bugs common |
| 593 |
|
with the <filename>make</> versions provided by commercial Unix |
| 594 |
|
vendors, GNU <filename>make</filename> (sometimes called |
| 595 |
|
<filename>gmake</filename>) should be preferred. This option |
| 596 |
|
provides a means for specifying the make program to be |
| 597 |
|
used.</para> |
| 598 |
|
</listitem> |
| 599 |
|
</varlistentry> |
| 600 |
|
|
| 601 |
|
</variablelist> |
| 602 |
|
|
| 603 |
|
<para>A successful run of <filename>genmake2</> will produce a |
| 604 |
|
<filename>Makefile</>, a <filename>PACKAGES_CONFIG.h</> file, and |
| 605 |
|
various convenience files used for the automatic differentiation |
| 606 |
|
process.</para> |
| 607 |
|
|
| 608 |
|
<para>In general, it is best to use <filename>genmake2</> on a "clean" |
| 609 |
|
directory that is free of all source (*.[F,f],*.[F,f]90) and header |
| 610 |
|
(*.h,*.inc) files. Generally, this can be accomplished in an |
| 611 |
|
"un-clean" directory by running "make CLEAN" followed by "make |
| 612 |
|
makefile".</para> |
| 613 |
|
|
| 614 |
|
</sect3> |
| 615 |
|
|
| 616 |
|
<sect3 id="makefile_use"> |
| 617 |
|
<title>Using the <filename>Makefile</></title> |
| 618 |
|
|
| 619 |
|
<para>Once a <filename>Makefile</> has been created using |
| 620 |
|
<filename>genmake2</>, one can build a "standard" (forward |
| 621 |
|
simulator) executable using:</para> |
| 622 |
|
|
| 623 |
|
<screen> |
| 624 |
|
$ make CLEAN |
| 625 |
|
$ make depend |
| 626 |
|
$ make |
| 627 |
|
</screen> |
| 628 |
|
|
| 629 |
|
<para>The "make CLEAN" step will remove any stale source files, include |
| 630 |
|
files, and links. It is strongly recommended for "un-clean" |
| 631 |
|
directories which may contain the (perhaps partial) results of |
| 632 |
|
previous builds. Such "debris" can interfere with the next stage of |
| 633 |
|
the build.</para> |
| 634 |
|
|
| 635 |
|
<para>The "make depend" step will create a large number of symbolic |
| 636 |
|
links from the local directory to the source file locations. It also |
| 637 |
|
parses these files and creates an extensive list of dependencies |
| 638 |
|
within the <filename>Makefile</> itself. The links that exist at this |
| 639 |
|
stage are mostly "large F" files (*.F and *.F90) that need to be |
| 640 |
|
processed by a C preprocessor ("CPP"). Since "make depend" edits the |
| 641 |
|
<filename>Makefile</>, it is important not to skip this step!</para> |
| 642 |
|
|
| 643 |
|
<para>The final "make" invokes the C preprocessor to produce the "little |
| 644 |
|
f" files (*.f and *.f90) and then compiles them to object code using |
| 645 |
|
the specified FORTRAN compiler and options. An intermediate script is |
| 646 |
|
often used during this stage to further process (usually, make simple |
| 647 |
|
substitutions) custom definitions such as variable types within the |
| 648 |
|
source files. This additional stage is necessary in order to overcome |
| 649 |
|
some of the inconsistencies in the sizes of objects (bytes) between |
| 650 |
|
different compilers. The result of the build process is an executable |
| 651 |
|
with the name <filename>mitgcmuv</>.</para> |
| 652 |
|
|
| 653 |
|
<para>In addition to the forward simulator described above, the |
| 654 |
|
<filename>Makefile</> also has a number of targets that can be used to |
| 655 |
|
produce various adjoint and tangent-linear builds for optimization and |
| 656 |
|
other parameter-sensitivity problems. The additional targets within |
| 657 |
|
the <filename>Makefile</> are:</para> |
| 658 |
|
|
| 659 |
|
<variablelist> |
| 660 |
|
|
| 661 |
|
<varlistentry> |
| 662 |
|
<term><filename>make adall</></term> |
| 663 |
|
<listitem> |
| 664 |
|
<para>This target produces an <filename>mitgcmuv_ad</> executable |
| 665 |
|
using the <filename>taf</> or <filename>staf</> adjoint |
| 666 |
|
compiler. See the <filename>genmake2</> "-adof" option for |
| 667 |
|
compiler selection.</para> |
| 668 |
|
</listitem> |
| 669 |
|
</varlistentry> |
| 670 |
|
|
| 671 |
|
<varlistentry> |
| 672 |
|
<term><filename>make ftlall</></term> |
| 673 |
|
<listitem> |
| 674 |
|
<para>Similar to <filename>make adall</> above, this |
| 675 |
|
produces...</para> |
| 676 |
|
</listitem> |
| 677 |
|
</varlistentry> |
| 678 |
|
|
| 679 |
|
</variablelist> |
| 680 |
|
|
| 681 |
|
<para>Please report any compilation failures or other build problems to |
| 682 |
|
the <email>MITgcm-support@mitgcm.org</email> list.</para> |
| 683 |
|
|
| 684 |
|
</sect3> |
| 685 |
|
|
| 686 |
|
</sect2> |
| 687 |
|
|
| 688 |
|
<sect2 id="verification"> |
| 689 |
|
<title>The Verification Suite</title> |
| 690 |
|
|
| 691 |
|
<para>The MITgcm CVS tree (within the <filename>$ROOTDIR/verification/</> |
| 692 |
|
directory) includes more than a dozen examples intended for regression |
| 693 |
|
testing. Each one of these example directories contains "known-good" |
| 694 |
|
output files along with all the input (including both code and data |
| 695 |
|
files) required for their re-calculation. These example directories are |
| 696 |
|
further broken down into sets of subdirectories |
| 697 |
|
(eg. <filename>/input</>, <filename>/code</>) intended to expedite the |
| 698 |
|
testing process.</para> |
| 699 |
|
|
| 700 |
|
<sect3 id="testreport"> |
| 701 |
|
<title>The <filename>testreport</> Utility</title> |
| 702 |
|
|
| 703 |
|
<para>Also included in <filename>$ROOTDIR/verification/</> are shell |
| 704 |
|
scripts for automated testing. The newest script (which was written |
| 705 |
|
to work with <filename>genmake2</>) is called <filename>testreport</>. |
| 706 |
|
This script can be used to build different versions of the MITgcm |
| 707 |
|
code, run the various examples, compare the output, and (if specified) |
| 708 |
|
email the results of each one of these tests to a central |
| 709 |
|
repository.</para> |
| 710 |
|
|
| 711 |
|
<para>On some systems, the testreport script can be run with a command |
| 712 |
|
line as simple as:</para> |
| 713 |
|
|
| 714 |
|
<screen> |
| 715 |
|
$ cd verification |
| 716 |
|
$ ./testreport -ieee |
| 717 |
|
</screen> |
| 718 |
|
|
| 719 |
|
<para>However, some systems (those lacking or wiht a broken "/bin/sh") |
| 720 |
|
may require an explicit shell invocation such as:</para> |
| 721 |
|
|
| 722 |
|
<screen> |
| 723 |
|
$ sh ./testreport -ieee -t 'exp0 exp4' |
| 724 |
|
$ /some/path/to/bash ./testreport -ieee -t 'ideal_2D_oce lab_sea natl_box' |
| 725 |
|
</screen> |
| 726 |
|
|
| 727 |
|
<para>The <filename>testreport</> script accepts a number of |
| 728 |
|
command-line options which can be listed using the <filename>-help</> |
| 729 |
|
option. The most important ones are:</para> |
| 730 |
|
|
| 731 |
|
<variablelist> |
| 732 |
|
|
| 733 |
|
<varlistentry> |
| 734 |
|
<term><filename>-ieee</></term> |
| 735 |
|
<listitem> |
| 736 |
|
<para>If allowed by the compiler (as defined in the "optfile"), |
| 737 |
|
use IEEE arithmetic. This option, along with the GCC compiler, |
| 738 |
|
is how the standard results were produced.</para> |
| 739 |
|
</listitem> |
| 740 |
|
</varlistentry> |
| 741 |
|
|
| 742 |
|
<varlistentry> |
| 743 |
|
<term><filename>-tdir TESTDIR</></term> |
| 744 |
|
<term><filename>-tdir 'TDIR1 TDIR2 [...]'</></term> |
| 745 |
|
<listitem> |
| 746 |
|
<para>This option specifies the test directory or list of test |
| 747 |
|
directories that should be used. Each of these entries should |
| 748 |
|
exactly (note: they are case sensitive!) match the names of |
| 749 |
|
directries in <filename>$ROOTDIR/verification/</>. If this |
| 750 |
|
option is omitted, then all directories that are properly |
| 751 |
|
formatted (that is, containing an <filename>input</> |
| 752 |
|
sub-directory and a <filename>results/output.txt</> file) will |
| 753 |
|
be used.</para> |
| 754 |
|
</listitem> |
| 755 |
|
</varlistentry> |
| 756 |
|
|
| 757 |
|
<varlistentry> |
| 758 |
|
<term><filename>-optfile=/PATH/FILENAME</></term> |
| 759 |
|
<term><filename>-optfile '/PATH/F1 [/PATH/F2 ...]'</></term> |
| 760 |
|
<listitem> |
| 761 |
|
<para>This specifies a list of "options files" that will be passed |
| 762 |
|
to <filename>genmake2</>. If multiple options files are used |
| 763 |
|
(say, to test different compilers or different sets of options |
| 764 |
|
for the same compiler), then each options file will be used with |
| 765 |
|
each of the test directories.</para> |
| 766 |
|
</listitem> |
| 767 |
|
</varlistentry> |
| 768 |
|
|
| 769 |
|
<varlistentry> |
| 770 |
|
<term><filename>-addr EMAIL</></term> |
| 771 |
|
<term><filename>-addr 'EMAIL1 EMAIL2 [...]'</></term> |
| 772 |
|
<listitem> |
| 773 |
|
<para>Send the results (namely, <filename>output.txt</>, |
| 774 |
|
<filename>genmake_local</>, <filename>genmake_state</>, and |
| 775 |
|
<filename>Makefile</>) to the specified email addresses. The |
| 776 |
|
results are gzipped, placed in a tar file, MIME encoded, and |
| 777 |
|
sent to the specified address. If no email addresses are |
| 778 |
|
specified, no mail is sent.</para> |
| 779 |
|
</listitem> |
| 780 |
|
</varlistentry> |
| 781 |
|
|
| 782 |
|
<varlistentry> |
| 783 |
|
<term><filename>-mpi</></term> |
| 784 |
|
<listitem> |
| 785 |
|
<para>If the necessary files |
| 786 |
|
(<filename>TESTDIR/code/CPP_EEOPTIONS.h_mpi</> and |
| 787 |
|
<filename>TESTDIR/code/SIZE.h_mpi</>) exist, then use them for an |
| 788 |
|
MPI--enabled run. Note that the use of MPI typically requires a |
| 789 |
|
special command option (see "-command" below) to invoke the MPI |
| 790 |
|
executable. Examples of PBS scripts using MPI with testreport can be |
| 791 |
|
found in the <ulink |
| 792 |
|
url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/"> |
| 793 |
|
MITgcm-contrib area</ulink></para> |
| 794 |
|
</listitem> |
| 795 |
|
</varlistentry> |
| 796 |
|
|
| 797 |
|
<varlistentry> |
| 798 |
|
<term><filename>-command='some command to run'</></term> |
| 799 |
|
<listitem> |
| 800 |
|
<para>For some tests, particularly MPI runs, the default "make |
| 801 |
|
output.txt" is not sufficient. This option allows a more general |
| 802 |
|
command (or shell script) to be invoked. Examples of PBS scripts |
| 803 |
|
using MPI with testreport can be found in the <ulink |
| 804 |
|
url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/"> |
| 805 |
|
MITgcm-contrib area</ulink></para> |
| 806 |
|
</listitem> |
| 807 |
|
</varlistentry> |
| 808 |
|
|
| 809 |
|
</variablelist> |
| 810 |
|
|
| 811 |
|
<para>The <filename>testreport</> script will write progress to the |
| 812 |
|
screen (stdout) as it runs. In addition, it will create a |
| 813 |
|
<filename>tr_out.txt</> file that contains a brief comparison of the |
| 814 |
|
current output with the "known-good" output.</para> |
| 815 |
|
|
| 816 |
|
</sect3> |
| 817 |
|
|
| 818 |
|
</sect2> |
| 819 |
|
|
| 820 |
|
|
| 821 |
|
<sect2 id="packages"> |
| 822 |
|
<title>Creating MITgcm Packages</title> |
| 823 |
|
|
| 824 |
|
<para>Optional parts of code have been separated from the MITgcmUV core |
| 825 |
|
driver code and organised into packages. The packaging structure |
| 826 |
|
provides a mechanism for maintaining suites of code, specific to |
| 827 |
|
particular classes of problems, in a way that is cleanly separated from |
| 828 |
|
the generic fluid dynamical engine.</para> |
| 829 |
|
|
| 830 |
|
<para>The MITgcmUV packaging structure is described below using generic |
| 831 |
|
package names ${pkg}. A concrete examples of a package is the code for |
| 832 |
|
implementing GM/Redi mixing. This code uses the package name</para> |
| 833 |
|
|
| 834 |
|
</sect2> |
| 835 |
|
|
| 836 |
|
</sect1> |
| 837 |
|
|
| 838 |
|
<sect1> |
| 839 |
|
<title>Chris's Notes...</title> |
| 840 |
|
|
| 841 |
|
<programlisting> |
| 842 |
|
MITgcmUV Packages |
| 843 |
|
================= |
| 844 |
|
|
| 845 |
|
Optional parts of code are separated from |
| 846 |
|
the MITgcmUV core driver code and organised into |
| 847 |
|
packages. The packaging structure provides a mechanism for |
| 848 |
|
maintaining suites of code, specific to particular |
| 849 |
|
classes of problem, in a way that is cleanly |
| 850 |
|
separated from the generic fluid dynamical engine. |
| 851 |
|
|
| 852 |
|
The MITgcmUV packaging structure is describe |
| 853 |
|
below using generic package names ${pkg}. |
| 854 |
|
A concrete examples of a package is the code |
| 855 |
|
for implementing GM/Redi mixing. This code uses |
| 856 |
|
the package name |
| 857 |
|
* ${PKG} = GMREDI |
| 858 |
|
* ${pkg} = gmredi |
| 859 |
|
* ${Pkg} = gmRedi |
| 860 |
|
|
| 861 |
|
Package states |
| 862 |
|
============== |
| 863 |
|
|
| 864 |
|
Packages can be any one of four states, included, |
| 865 |
|
excluded, enabled, disabled as follows: |
| 866 |
|
|
| 867 |
|
included(excluded) compile time state which |
| 868 |
|
includes(excludes) package |
| 869 |
|
code and routine calls from |
| 870 |
|
compilation/linking etc... |
| 871 |
|
|
| 872 |
|
enabled(disabled) run-time state which |
| 873 |
|
enables(disables) package code |
| 874 |
|
execution. |
| 875 |
|
|
| 876 |
|
Every call to a ${pkg}_... routine from outside the package |
| 877 |
|
should be placed within both a |
| 878 |
|
#ifdef ALLOW_${PKG} ... block and a |
| 879 |
|
if ( use${Pkg} ) ... then block. |
| 880 |
|
Package states are generally not expected to change during |
| 881 |
|
a model run. |
| 882 |
|
|
| 883 |
|
Package structure |
| 884 |
|
================= |
| 885 |
|
|
| 886 |
|
o Each package gets its runtime configuration |
| 887 |
|
parameters from a file named "data.${pkg}" |
| 888 |
|
Package runtime config. options are imported |
| 889 |
|
into a common block held in a header file |
| 890 |
|
called "${PKG}.h". |
| 891 |
|
Note: In some packages, the header file "${PKG}.h" is splitted |
| 892 |
|
into "${PKG}_PARAMS.h" that contains the package parameters and |
| 893 |
|
${PKG}_VARS.h" for the field arrays. |
| 894 |
|
|
| 895 |
|
o The core driver part of the model can check |
| 896 |
|
for runtime enabling or disabling of individual packages |
| 897 |
|
through logical flags use${Pkg}. |
| 898 |
|
The information is loaded from a |
| 899 |
|
global package setup file called "data.pkg". |
| 900 |
|
The use${Pkg} flags are not used within |
| 901 |
|
individual packages. |
| 902 |
|
|
| 903 |
|
o Included in "${PKG}.h" is a logical flag |
| 904 |
|
called ${Pkg}IsOn. The "${PKG}.h" header file can be imported |
| 905 |
|
by other packages to check dependencies and requirements |
| 906 |
|
from other packages ( see "Package Boot Sequence" section). |
| 907 |
|
NOTE: This procedure is not presently implemented, |
| 908 |
|
----- neither for kpp nor for gmRedi. |
| 909 |
|
|
| 910 |
|
CPP Flags |
| 911 |
|
========= |
| 912 |
|
|
| 913 |
|
1. Within the core driver code flags of the form |
| 914 |
|
ALLOW_${PKG} are used to include or exclude |
| 915 |
|
whole packages. The ALLOW_${PKG} flags are included |
| 916 |
|
from a PACKAGES_CONFIG.h file that is automatically |
| 917 |
|
generated by genmake2 (see genmake2 section). |
| 918 |
|
held in-line in the CPP_OPTIONS.h header file. |
| 919 |
|
e.g. |
| 920 |
|
|
| 921 |
|
Core model code ..... |
| 922 |
|
|
| 923 |
|
#include "PACKAGES_CONFIG.h" |
| 924 |
|
#include "CPP_OPTIONS.h" |
| 925 |
|
: |
| 926 |
|
: |
| 927 |
|
: |
| 928 |
|
|
| 929 |
|
#ifdef ALLOW_${PKG} |
| 930 |
|
if ( use${Pkg} ) CALL ${PKG}_DO_SOMETHING(...) |
| 931 |
|
#endif |
| 932 |
|
|
| 933 |
|
2. Within an individual package a header file, |
| 934 |
|
"${PKG}_OPTIONS.h", is used to set CPP flags |
| 935 |
|
specific to that package. It also includes |
| 936 |
|
"PACKAGES_CONFIG.h" and "CPP_OPTIONS.h". |
| 937 |
|
|
| 938 |
|
|
| 939 |
|
Package Boot Sequence |
| 940 |
|
===================== |
| 941 |
|
|
| 942 |
|
Calls to package routines within the core code timestepping |
| 943 |
|
loop can vary. However, all packages follow a required |
| 944 |
|
"boot" sequence outlined here: |
| 945 |
|
|
| 946 |
|
1. S/R PACKAGES_BOOT() |
| 947 |
|
: |
| 948 |
|
CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... ) |
| 949 |
|
|
| 950 |
|
|
| 951 |
|
2. S/R PACKAGES_READPARMS() |
| 952 |
|
: |
| 953 |
|
#ifdef ALLOW_${PKG} |
| 954 |
|
if ( use${Pkg} ) |
| 955 |
|
& CALL ${PKG}_READPARMS( retCode ) |
| 956 |
|
#endif |
| 957 |
|
|
| 958 |
|
3. S/R PACKAGES_INIT_FIXED() |
| 959 |
|
: |
| 960 |
|
#ifdef ALLOW_${PKG} |
| 961 |
|
if ( use${Pkg} ) |
| 962 |
|
& CALL ${PKG}_INIT_FIXED( retCode ) |
| 963 |
|
#endif |
| 964 |
|
|
| 965 |
|
4. S/R PACKAGES_CHECK() |
| 966 |
|
: |
| 967 |
|
#ifdef ALLOW_${PKG} |
| 968 |
|
if ( use${Pkg} ) |
| 969 |
|
& CALL ${PKG}_CHECK( retCode ) |
| 970 |
|
#else |
| 971 |
|
if ( use${Pkg} ) |
| 972 |
|
& CALL PACKAGES_CHECK_ERROR('${PKG}') |
| 973 |
|
#endif |
| 974 |
|
|
| 975 |
|
5. S/R PACKAGES_INIT_VARIABLES() |
| 976 |
|
: |
| 977 |
|
#ifdef ALLOW_${PKG} |
| 978 |
|
if ( use${Pkg} ) |
| 979 |
|
& CALL ${PKG}_INIT_VARIA( ) |
| 980 |
|
#endif |
| 981 |
|
|
| 982 |
|
Package Output |
| 983 |
|
============== |
| 984 |
|
6. S/R DO_THE_MODEL_IO |
| 985 |
|
|
| 986 |
|
#ifdef ALLOW_${PKG} |
| 987 |
|
if ( use${Pkg} ) |
| 988 |
|
& CALL ${PKG}_OUTPUT( ) |
| 989 |
|
#endif |
| 990 |
|
|
| 991 |
|
7. S/R PACKAGES_WRITE_PICKUP() |
| 992 |
|
|
| 993 |
|
#ifdef ALLOW_${PKG} |
| 994 |
|
if ( use${Pkg} ) |
| 995 |
|
& CALL ${PKG}_WRITE_PICKUP( ) |
| 996 |
|
#endif |
| 997 |
|
|
| 998 |
|
Description |
| 999 |
|
=========== |
| 1000 |
|
|
| 1001 |
|
- ${PKG}_READPARMS() |
| 1002 |
|
is responsible for reading |
| 1003 |
|
in the package parameters file data.${pkg}, and storing |
| 1004 |
|
the package parameters in "${PKG}.h" (or in "${PKG}_PARAMS.h"). |
| 1005 |
|
-> called from INITIALISE_FIXED in PACKAGES_READPARMS |
| 1006 |
|
|
| 1007 |
|
- ${PKG}_INIT_FIXED() |
| 1008 |
|
is responsible for completing the internal setup of a package. |
| 1009 |
|
-> called from INITIALISE_FIXED in PACKAGES_INIT_FIXED |
| 1010 |
|
note: 1) some pkg use instead: |
| 1011 |
|
CALL ${PKG}_INITIALISE ( or the old form CALL ${PKG}_INIT ) |
| 1012 |
|
2) for simple pkg setup, this part is done inside ${PKG}_READPARMS |
| 1013 |
|
|
| 1014 |
|
- ${PKG}_CHECK() |
| 1015 |
|
is responsible for validating |
| 1016 |
|
basic package setup and inter-package dependencies. |
| 1017 |
|
${PKG}_CHECK can import other package parameters it may |
| 1018 |
|
need to check. This is done through header files "${PKG}.h". |
| 1019 |
|
It is assumed that parameters owned by other packages |
| 1020 |
|
will not be reset during ${PKG}_CHECK(). |
| 1021 |
|
-> called from INITIALISE_FIXED in PACKAGES_CHECK |
| 1022 |
|
|
| 1023 |
|
- ${PKG}_INIT_VARIA() |
| 1024 |
|
is responsible for fill-in all package variables with an initial value. |
| 1025 |
|
Contains eventually a call to ${PKG}_READ_PICKUP that will read |
| 1026 |
|
from a pickup file the package variables required to restart the model. |
| 1027 |
|
This routine is called after the core model state has been completely |
| 1028 |
|
initialised but before the core model timestepping starts. |
| 1029 |
|
-> called from INITIALISE_VARIA in PACKAGES_INIT_VARIABLES |
| 1030 |
|
note: the name ${PKG}_INIT_VARIA is not yet standard and some pkg |
| 1031 |
|
use for e.g. ${PKG}_INI_VARS, ${PKG}_INIT_VARIABLES, or the old |
| 1032 |
|
form ${PKG}_INIT |
| 1033 |
|
|
| 1034 |
|
- ${PKG}_OUTPUT( ) |
| 1035 |
|
is responsible for writing time-average fields to output files |
| 1036 |
|
(but the cumulating step is done within the package main S/R). |
| 1037 |
|
Can also contain other diagnostics (.e.g. CALL ${PKG}_MONITOR) |
| 1038 |
|
and write snap-shot fields that are hold in common blocks. Other |
| 1039 |
|
temporary fields are directly dump to file where they are available. |
| 1040 |
|
NOTE: 1) the S/R old name ${PKG}_DIAGS is used in some packages |
| 1041 |
|
but is beeing replaced by ${PKG}_OUTPUT |
| 1042 |
|
to avoid confusion with pkg/diagnostics functionality. |
| 1043 |
|
2) the output part is not yet in a standard form and might still |
| 1044 |
|
evolve a lot. |
| 1045 |
|
-> called within DO_THE_MODEL_IO |
| 1046 |
|
|
| 1047 |
|
- ${PKG}_WRITE_PICKUP() |
| 1048 |
|
is responsible for writing a package pickup file when necessary for |
| 1049 |
|
a restart. (found also the old name: ${PKG}_WRITE_CHECKPOINT ) |
| 1050 |
|
-> called from FORWARD_STEP and THE_MODEL_MAIN in PACKAGES_WRITE_PICKUP |
| 1051 |
|
|
| 1052 |
|
Summary |
| 1053 |
|
======= |
| 1054 |
|
|
| 1055 |
|
- CPP options: |
| 1056 |
|
----------------------- |
| 1057 |
|
* ALLOW_${PKG} include/exclude package for compilation |
| 1058 |
|
|
| 1059 |
|
- FORTRAN logical: |
| 1060 |
|
----------------------- |
| 1061 |
|
* use${Pkg} enable package for execution at runtime |
| 1062 |
|
-> declared in PARAMS.h |
| 1063 |
|
* ${Pkg}IsOn for package cross-dependency check |
| 1064 |
|
-> declared in ${PKG}.h |
| 1065 |
|
N.B.: Not presently used! |
| 1066 |
|
|
| 1067 |
|
- header files |
| 1068 |
|
----------------------- |
| 1069 |
|
* ${PKG}_OPTIONS.h has further package-specific CPP options |
| 1070 |
|
* ${PKG}.h package-specific common block variables, fields |
| 1071 |
|
or ${PKG}_PARAMS.h package-specific common block parameters |
| 1072 |
|
and ${PKG}_VARS.h package-specific common block fields |
| 1073 |
|
|
| 1074 |
|
- FORTRAN source files |
| 1075 |
|
----------------------- |
| 1076 |
|
* ${pkg}_readparms.F reads parameters from file data.${pkg} |
| 1077 |
|
* ${pkg}_init_fixed.F complete the package setup |
| 1078 |
|
* ${pkg}_check.F checks package dependencies and consistencies |
| 1079 |
|
* ${pkg}_init_varia.F initialises package-related fields |
| 1080 |
|
* ${pkg}_... .F package source code |
| 1081 |
|
* ${pkg}_output.F write output to file. |
| 1082 |
|
* ${pkg}_write_pickup.F write a package pickup file to restart the model |
| 1083 |
|
|
| 1084 |
|
New: Subroutine in one package (pkgA) that only contains code which |
| 1085 |
|
is connected to a 2nd package (pkgB) (e.g.: gmredi_diagnostics_init.F) |
| 1086 |
|
will be named: pkgA_pkgB_something.F |
| 1087 |
|
|
| 1088 |
|
- parameter file |
| 1089 |
|
----------------------- |
| 1090 |
|
* data.${pkg} parameter file |
| 1091 |
|
</programlisting> |
| 1092 |
|
|
| 1093 |
|
</sect1> |
| 1094 |
|
|
| 1095 |
|
|
| 1096 |
<sect1 id="documentation"> |
<sect1 id="documentation"> |
| 1097 |
<title>Editing the Documentation</title> |
<title>Editing the Documentation</title> |
| 1098 |
|
|
| 1099 |
<sect2 id="documentation_getting"> |
<sect2 id="documentation_getting"> |
| 1100 |
<title>Getting the Docs and Code</title> |
<title>Getting the Docs and Code</title> |
| 1101 |
|
|
| 1102 |
<para>The first step towards editing the documentation is to |
<para>The first step towards editing the documentation is to checkout a |
| 1103 |
checkout a copy of code, docs, and build scripts from the CVS |
copy of code, docs, and build scripts from the CVS server using:</para> |
| 1104 |
server using:</para> |
|
| 1105 |
|
<screen> |
| 1106 |
<screen> |
$ export CVS_RSH=ssh |
| 1107 |
$ export CVS_RSH=ssh |
$ export CVSROOT=':ext:NAME@mitgcm.org:/u/gcmpack' |
| 1108 |
$ export CVSROOT=':ext:auden.lcs.mit.edu:/u/u3/gcmpack' |
$ mkdir scratch |
| 1109 |
$ mkdir scratch |
$ cvs co -P MITgcm manual mitgcm.org |
| 1110 |
$ cvs co MITgcm manual mitgcm.org |
</screen> |
| 1111 |
</screen> |
|
| 1112 |
|
<para>These commands extract the necessary information from the CVS server |
| 1113 |
<para>These commands extract the necessary information from the |
and create a temporary (called <filename>scratch</filename>) directory for |
| 1114 |
CVS server and create a temporary (called |
the storage of the HTML and other files that will be created. Please note |
| 1115 |
<filename>scratch</filename>) directory for the storage of the |
that you must either create <filename>scratch</filename> as shown or edit |
| 1116 |
HTML and other files that will be created. Please note that you |
the various <filename>Makefile</filename>s and scripts used to create the |
| 1117 |
must either create <filename>scratch</filename> as shown or edit |
documentation.</para> |
|
the various <filename>Makefile</filename>s and scripts used to |
|
|
create the documentation.</para> |
|
| 1118 |
</sect2> |
</sect2> |
| 1119 |
|
|
| 1120 |
<sect2> |
<sect2> |
| 1121 |
<title>Editing</title> |
<title>Editing the Documentation</title> |
| 1122 |
|
|
| 1123 |
<para>The documentation is contained in the |
<para>The documentation is contained in the <filename>manual</filename> |
| 1124 |
<filename>manual</filename> directory in a raw LaTeX format. |
directory in a raw LaTeX format. The main document is |
| 1125 |
The main document is <filename>manual.tex</filename> and it uses |
<filename>manual.tex</filename> and it uses <command>\input{}</command>s |
| 1126 |
<command>\input{}</command>s to include the chapters and |
to include the chapters and subsections.</para> |
| 1127 |
subsections.</para> |
|
| 1128 |
|
<para>Since the same LaTeX source is used to produce PostScript, PDF, and |
| 1129 |
<para>Since the same LaTeX source is used to produce PostScript, |
HTML output, care should be taken to follow certain conventions. Two of |
| 1130 |
PDF, and HTML output, care should be taken to follow certain |
the most important are the usage of the <command>\filelink{}{}</command> |
| 1131 |
conventions. Two of the most important are the usage of the |
and <command>\varlink{}{}</command> commands. Both of these commands have |
| 1132 |
<command>\filelink{}{}</command> and |
been defined to simplify the connection between the automatically |
| 1133 |
<command>\varlink{}{}</command> commands. Both of these |
generated ("code browser") HTML and the HTML version of the manual |
| 1134 |
commands have been defined to simplify the connection between |
produced by LaTeX2HTML. They each take two arguments (corresponding to |
| 1135 |
the automatically generated ("code browser") HTML and the HTML |
the contents of the two sets of curly braces) which are the text that the |
| 1136 |
version of the manual produced by LaTeX2HTML. They each take |
author wishes to be "wrapped" within the link, and a specially formatted |
| 1137 |
two arguments (corresponding to the contents of the two sets of |
link thats relative to the <filename>MITgcm</filename> directory within |
| 1138 |
curly braces) which are the text that the author wishes to be |
the CVS tree.</para> |
|
"wrapped" within the link, and a specially formatted link thats |
|
|
relative to the <filename>MITgcm</filename> directory within the |
|
|
CVS tree.</para> |
|
| 1139 |
|
|
| 1140 |
<para>The result is a command that resembles either</para> |
<para>The result is a command that resembles either</para> |
| 1141 |
|
|
| 1163 |
</sect2> |
</sect2> |
| 1164 |
|
|
| 1165 |
<sect2> |
<sect2> |
| 1166 |
<title>Building</title> <para>Given the directory structure of |
<title>Building the Documentation</title> |
| 1167 |
<xref linkend="documentation_getting">, the entire documentation |
|
| 1168 |
for the web site can be built using:</para> |
<para>Given the directory structure of <xref |
| 1169 |
|
linkend="documentation_getting">, the entire documentation for the web |
| 1170 |
|
site can be built using:</para> |
| 1171 |
|
|
| 1172 |
<screen> |
<screen> |
| 1173 |
$ cd mitgcm.org/devel/buildweb |
$ cd mitgcm.org/devel/buildweb |
| 1174 |
$ make All |
$ make All |
| 1175 |
</screen> |
</screen> |
| 1176 |
|
|
| 1177 |
<para>Which builds the PDF from the LaTeX source, creates the |
<para>Which builds the PDF from the LaTeX source, creates the HTML output |
| 1178 |
HTML output from the LaTeX source, parses the FORTRAN code base |
from the LaTeX source, parses the FORTRAN code base to produce a |
| 1179 |
to produce a hyperlinked HTML version of the source, and then |
hyperlinked HTML version of the source, and then determines the |
| 1180 |
determines the cross-linking between the various HTML |
cross-linking between the various HTML components.</para> |
| 1181 |
components.</para> |
|
| 1182 |
|
<para>If there are no errors, the result of the build process (which can |
| 1183 |
<para>If there are no errors, the result of the build process |
take 30+ minutes on a P4/2.5Ghz) will be contained within a single |
| 1184 |
(which can take 30+ minutes on a P4/2.5Ghz) will be contained |
directory called <filename>scratch/dev_docs</filename>. This is a freshly |
| 1185 |
within a single directory called |
built version of the entire on-line users manual. If you have the correct |
| 1186 |
<filename>scratch/dev_docs</filename>. This is a freshly built |
permissions, it can be directly copied to the web server area:</para> |
|
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> |
|
| 1187 |
|
|
| 1188 |
<screen> |
<screen> |
| 1189 |
$ mv scratch/dev_docs /u/u0/httpd/html |
$ mv scratch/dev_docs /u/u0/httpd/html |
| 1190 |
</screen> |
</screen> |
| 1191 |
|
|
| 1192 |
<para>and the update is complete.</para> |
<para>and the update is complete.</para> |
| 1195 |
|
|
| 1196 |
</sect1> |
</sect1> |
| 1197 |
|
|
|
|
|
|
|
|
| 1198 |
</article> |
</article> |
| 1199 |
|
|
| 1200 |
|
|
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| 
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| 
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