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<article id="MITgcm-Development-HOWTO"> |
<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> |
7 |
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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> |
25 |
|
<revision> |
26 |
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<revnumber>0.02</revnumber> |
27 |
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<date>2010-01-21</date> |
28 |
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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> |
32 |
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</revision> |
33 |
</revhistory> |
</revhistory> |
34 |
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35 |
<abstract> |
<abstract> |
45 |
<sect2> |
<sect2> |
46 |
<title>New Versions of This Document</title> <para>You can |
<title>New Versions of This Document</title> <para>You can |
47 |
obtain the latest version of this document <ulink |
obtain the latest version of this document <ulink |
48 |
url="http://mitgcm.org/dev_docs/devel_HOWTO/">online</ulink> in |
url="http://mitgcm.org/public/docs.html">online</ulink> in |
49 |
various formats.</para> |
various formats.</para> |
50 |
</sect2> |
</sect2> |
51 |
<sect2> |
<sect2> |
63 |
<sect2> |
<sect2> |
64 |
<title>User Manual</title> |
<title>User Manual</title> |
65 |
|
|
66 |
<para>Before jumping into |
<para>Before jumping into development, please familiarize yourself with |
67 |
development, please familiarize yourself with the MITgcm user |
the <ulink url="http://mitgcm.org/public/docs.html"> MITgcm user manual |
68 |
manual which is available <ulink |
</ulink>. This document contains volumes of useful information and is |
69 |
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 |
|
|
here by reference.</para> |
|
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|
|
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<para>Also, a "snapshot" or<ulink |
<!-- |
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|
<para>Also, a "snapshot" or <ulink |
73 |
url="http://mitgcm.org/dev_docs/">development version</ulink> of |
url="http://mitgcm.org/dev_docs/">development version</ulink> of |
74 |
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> |
78 |
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79 |
<sect2> |
<sect2> |
128 |
doc tags -- connect to real docs? |
doc tags -- connect to real docs? |
129 |
eesupp cnh? |
eesupp cnh? |
130 |
exe ecco user build |
exe ecco user build |
131 |
*- jobs runtime shell scripts for |
,- jobs runtime shell scripts for |
132 |
| various platforms |
| various platforms |
133 |
| lsopt line search |
| lsopt line search |
134 |
m| model main dynamics (core) |
m| model main dynamics (core) |
135 |
e| optimization_drivers ? |
e| optimization_drivers ? |
136 |
r| optim line search interface |
r| optim line search interface |
137 |
g| pkg alternate and optional numerics, etc. |
g| pkg alternate and optional numerics, etc. |
138 |
e*- tools |
e|- tools |
139 |
?| tutorial_examples documented tests |
?| tutorial_examples documented tests |
140 |
| only populated on release1 branch |
| only populated on release1 branch |
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| and not validated during "testscript" |
| and not validated during "testreport" |
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*- utils |
'- utils |
143 |
verification std tests |
verification std tests |
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<title>Branches</title> |
<title>Branches</title> |
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|
|
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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/doc/tag-index?view=graph"> |
194 |
tree</ulink>, the MITgcm codebase is split into to two branches |
ViewCVS-generated tree</ulink>, the MITgcm codebase is split into to two |
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or "lines" under which development proceeds. These two lines |
branches or "lines" under which development proceeds. These two lines are |
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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 |
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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 |
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composed of files from the same codebase. |
the same codebase. |
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</para> |
</para> |
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|
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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 |
204 |
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. |
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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 |
207 |
tutorials, and/or examples contained within a release branch) is |
branch) is allowed to continue along the MAIN and ecco lines.</para> |
|
allowed to continue along the MAIN and ecco lines.</para> |
|
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</sect2> |
</sect2> |
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|
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<sect2> |
<sect2> |
211 |
<title>Tagging</title> |
<title>Tagging</title> |
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|
|
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<para>The intent of tagging is to create "known-good" |
<para>The intent of tagging is to create "known-good" checkpoints that |
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checkpoints that developers can use as references. |
developers can use as references. Traditionally, MITgcm tagging has |
215 |
Traditionally, MITgcm tagging has maintained the following |
maintained the following conventions:</para> |
|
conventions:</para> |
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<orderedlist> |
<orderedlist> |
218 |
<listitem> |
<listitem> |
219 |
<para>Developer checks out code into a local CVS-managed |
<para>Developer checks out code into a local CVS-managed directory, |
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directory, makes various changes/additions, tests these |
makes various changes/additions, tests these edits, and eventually |
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edits, and eventually reaches a point where (s)he is |
reaches a point where (s)he is satisfied that the changes form a new |
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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> |
|
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</listitem> |
</listitem> |
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|
|
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<listitem> |
<listitem> |
226 |
<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"> |
228 |
shell script to see if any problems are introduced. While |
testreport</ulink> shell script to see if any problems are introduced. |
229 |
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 |
231 |
gross errors have been introduced. |
have been introduced. |
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</para> |
</para> |
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</listitem> |
</listitem> |
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|
|
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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 |
242 |
checkpoint number and Y is a letter) to the <ulink |
number and Y is a letter) to the <ulink |
243 |
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"> |
244 |
file and checks it into the CVS repository</para> |
tag-index</ulink> file and checks it into the CVS |
245 |
|
repository</para> |
246 |
</listitem> |
</listitem> |
247 |
<listitem> |
<listitem> |
248 |
<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 |
250 |
describing what the changes are along with a matching |
changes are along with a matching "checkpointXY_post" entry</para> |
|
"checkpointXY_post" entry</para> |
|
251 |
</listitem> |
</listitem> |
252 |
</orderedlist> |
</orderedlist> |
253 |
</listitem> |
</listitem> |
254 |
</orderedlist> |
</orderedlist> |
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|
|
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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 |
257 |
development checkpoints with comments which resembles:</para> |
checkpoints with comments which resembles:</para> |
258 |
|
|
259 |
<programlisting> |
<programlisting> |
260 |
checkpoint50e_post |
checkpoint50e_post |
276 |
checkpoint50d_pre |
checkpoint50d_pre |
277 |
</programlisting> |
</programlisting> |
278 |
|
|
279 |
<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 |
280 |
the code development. For example, bugs can be traced to |
development. For example, bugs can be traced to individual sets of CVS |
281 |
individual sets of CVS checkins based upon their first |
checkins based upon their first appearance when comparing the results from |
282 |
appearance when comparing the results from different |
different checkpoints.</para> |
|
checkpoints.</para> |
|
283 |
|
|
284 |
</sect2> |
</sect2> |
285 |
</sect1> |
</sect1> |
291 |
<sect2 id="documentation_getting"> |
<sect2 id="documentation_getting"> |
292 |
<title>Getting the Docs and Code</title> |
<title>Getting the Docs and Code</title> |
293 |
|
|
294 |
<para>The first step towards editing the documentation is to |
<para>The first step towards editing the documentation is to checkout a |
295 |
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> |
|
server using:</para> |
|
296 |
|
|
297 |
<screen> |
<screen> |
298 |
$ export CVS_RSH=ssh |
$ export CVS_RSH=ssh |
299 |
$ export CVSROOT=':ext:auden.lcs.mit.edu:/u/u3/gcmpack' |
$ export CVSROOT=':ext:NAME@mitgcm.org:/u/gcmpack' |
300 |
$ mkdir scratch |
$ mkdir scratch |
301 |
$ cvs co MITgcm manual mitgcm.org |
$ cvs co -P MITgcm manual mitgcm.org |
302 |
</screen> |
</screen> |
303 |
|
|
304 |
<para>These commands extract the necessary information from the |
<para>These commands extract the necessary information from the CVS server |
305 |
CVS server and create a temporary (called |
and create a temporary (called <filename>scratch</filename>) directory for |
306 |
<filename>scratch</filename>) directory for the storage of the |
the storage of the HTML and other files that will be created. Please note |
307 |
HTML and other files that will be created. Please note that you |
that you must either create <filename>scratch</filename> as shown or edit |
308 |
must either create <filename>scratch</filename> as shown or edit |
the various <filename>Makefile</filename>s and scripts used to create the |
309 |
the various <filename>Makefile</filename>s and scripts used to |
documentation.</para> |
|
create the documentation.</para> |
|
310 |
</sect2> |
</sect2> |
311 |
|
|
312 |
<sect2> |
<sect2> |
313 |
<title>Editing</title> |
<title>Editing the Documentation</title> |
314 |
|
|
315 |
<para>The documentation is contained in the |
<para>The documentation is contained in the <filename>manual</filename> |
316 |
<filename>manual</filename> directory in a raw LaTeX format. |
directory in a raw LaTeX format. The main document is |
317 |
The main document is <filename>manual.tex</filename> and it uses |
<filename>manual.tex</filename> and it uses <command>\input{}</command>s |
318 |
<command>\input{}</command>s to include the chapters and |
to include the chapters and subsections.</para> |
319 |
subsections.</para> |
|
320 |
|
<para>Since the same LaTeX source is used to produce PostScript, PDF, and |
321 |
<para>Since the same LaTeX source is used to produce PostScript, |
HTML output, care should be taken to follow certain conventions. Two of |
322 |
PDF, and HTML output, care should be taken to follow certain |
the most important are the usage of the <command>\filelink{}{}</command> |
323 |
conventions. Two of the most important are the usage of the |
and <command>\varlink{}{}</command> commands. Both of these commands have |
324 |
<command>\filelink{}{}</command> and |
been defined to simplify the connection between the automatically |
325 |
<command>\varlink{}{}</command> commands. Both of these |
generated ("code browser") HTML and the HTML version of the manual |
326 |
commands have been defined to simplify the connection between |
produced by LaTeX2HTML. They each take two arguments (corresponding to |
327 |
the automatically generated ("code browser") HTML and the HTML |
the contents of the two sets of curly braces) which are the text that the |
328 |
version of the manual produced by LaTeX2HTML. They each take |
author wishes to be "wrapped" within the link, and a specially formatted |
329 |
two arguments (corresponding to the contents of the two sets of |
link thats relative to the <filename>MITgcm</filename> directory within |
330 |
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> |
|
331 |
|
|
332 |
<para>The result is a command that resembles either</para> |
<para>The result is a command that resembles either</para> |
333 |
|
|
355 |
</sect2> |
</sect2> |
356 |
|
|
357 |
<sect2> |
<sect2> |
358 |
<title>Building</title> <para>Given the directory structure of |
<title>Building the Documentation</title> |
359 |
<xref linkend="documentation_getting">, the entire documentation |
|
360 |
for the web site can be built using:</para> |
<para>Given the directory structure of <xref |
361 |
|
linkend="documentation_getting">, the entire documentation for the web |
362 |
|
site can be built using:</para> |
363 |
|
|
364 |
<screen> |
<screen> |
365 |
$ cd mitgcm.org/devel/buildweb |
$ cd mitgcm.org/devel/buildweb |
366 |
$ make All |
$ make All |
367 |
</screen> |
</screen> |
368 |
|
|
369 |
<para>Which builds the PDF from the LaTeX source, creates the |
<para>Which builds the PDF from the LaTeX source, creates the HTML output |
370 |
HTML output from the LaTeX source, parses the FORTRAN code base |
from the LaTeX source, parses the FORTRAN code base to produce a |
371 |
to produce a hyperlinked HTML version of the source, and then |
hyperlinked HTML version of the source, and then determines the |
372 |
determines the cross-linking between the various HTML |
cross-linking between the various HTML components.</para> |
373 |
components.</para> |
|
374 |
|
<para>If there are no errors, the result of the build process (which can |
375 |
<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 |
376 |
(which can take 30+ minutes on a P4/2.5Ghz) will be contained |
directory called <filename>scratch/dev_docs</filename>. This is a freshly |
377 |
within a single directory called |
built version of the entire on-line users manual. If you have the correct |
378 |
<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> |
|
379 |
|
|
380 |
<screen> |
<screen> |
381 |
$ mv scratch/dev_docs /u/u0/httpd/html |
$ mv scratch/dev_docs /u/u0/httpd/html |
382 |
</screen> |
</screen> |
383 |
|
|
384 |
<para>and the update is complete.</para> |
<para>and the update is complete.</para> |
387 |
|
|
388 |
</sect1> |
</sect1> |
389 |
|
|
390 |
|
<sect1 id="coding"> |
391 |
|
<title>Coding for MITgcm</title> |
392 |
|
|
393 |
|
<sect2 id="build_tools"> |
394 |
|
<title>Build Tools</title> |
395 |
|
|
396 |
|
<para>Many Open Source projects use the "GNU Autotools" to help streamline |
397 |
|
the build process for various Unix and Unix-like architectures. For a |
398 |
|
user, the result is the common "configure" (that is, |
399 |
|
"<filename>./configure && make && make install</filename>") commands. |
400 |
|
For MITgcm, the process is similar. Typical commands are:</para> |
401 |
|
|
402 |
|
<screen> |
403 |
|
$ genmake -mods=../code |
404 |
|
$ make depend |
405 |
|
$ make |
406 |
|
</screen> |
407 |
|
|
408 |
|
<para>The following sections describe the individual steps in the build |
409 |
|
process.</para> |
410 |
|
|
411 |
|
<sect3 id="genmake"> |
412 |
|
<title>The <filename>genmake2</> Utility</title> |
413 |
|
|
414 |
|
<para><emphasis>Please note that the older <filename>genmake</> is |
415 |
|
deprecated and will eventually be replaced by <filename>genmake2</>. |
416 |
|
This HOWTO only describes the newer tool.</emphasis></para> |
417 |
|
|
418 |
|
<para>The first step in any MITgcm build is to create a Unix-style |
419 |
|
<filename>Makefile</filename> which will be parsed by |
420 |
|
<filename>make</filename> to specify how to compile the MITgcm source |
421 |
|
files. For more detailed descriptions of what the make tools are and |
422 |
|
how they are used, please see:</para> |
423 |
|
|
424 |
|
<itemizedlist> |
425 |
|
<listitem> |
426 |
|
<para><ulink url="http://www.gnu.org/software/make/make.html"> |
427 |
|
http://www.gnu.org/software/make/make.html</></para> |
428 |
|
</listitem> |
429 |
|
<listitem> |
430 |
|
<para><ulink url="http://www.oreilly.com/catalog/make2/"> |
431 |
|
http://www.oreilly.com/catalog/make2/</></para> |
432 |
|
</listitem> |
433 |
|
</itemizedlist> |
434 |
|
|
435 |
|
<para>Genmake can often be invoked successfully with a command line as |
436 |
|
simple as:</para> |
437 |
|
|
438 |
|
<screen> |
439 |
|
$ genmake2 -mods=../code |
440 |
|
</screen> |
441 |
|
|
442 |
|
<para>However, some systems (particularly commercial Unixes that lack a |
443 |
|
more modern "/bin/sh" implementation or that have shells installed in |
444 |
|
odd locations) may require an explicit shell invocation such as one of |
445 |
|
the following: </para> |
446 |
|
|
447 |
|
<screen> |
448 |
|
$ /usr/bin/sh genmake2 -make=gmake -mods=../code |
449 |
|
$ /opt/gnu/bin/bash genmake2 -ieee -make=/usr/local/bin/gmake -mods=../code |
450 |
|
</screen> |
451 |
|
|
452 |
|
<para>The genmake2 code has been written in a Bourne and BASH (v1) |
453 |
|
compatible syntax so it should work with most "sh" and all recent "bash" |
454 |
|
implementations.</para> |
455 |
|
|
456 |
|
<para>As the name implies, <filename>genmake2</filename> generates a |
457 |
|
<filename>Makefile</filename>. It does so by first parsing the |
458 |
|
information supplied from the following sources</para> |
459 |
|
|
460 |
|
<orderedlist> |
461 |
|
<listitem> |
462 |
|
<para>a <filename>gemake_local</filename> file in the current |
463 |
|
directory</para> |
464 |
|
</listitem> |
465 |
|
<listitem> |
466 |
|
<para>directly from command-line options</para> |
467 |
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</listitem> |
468 |
|
<listitem> |
469 |
|
<para>an "options file" as specified by the command-line option |
470 |
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<filename>-optfile='FILENAME'</filename></para> |
471 |
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</listitem> |
472 |
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</orderedlist> |
473 |
|
|
474 |
|
<para>then checking certain dependency rules (the package dependencies), |
475 |
|
and finally writing a <filename>Makefile</filename> based upon the |
476 |
|
source code that it finds. For convenience within various Unix |
477 |
|
shells, <filename>genmake2</> supports both "long"- and "short"-style |
478 |
|
options. A complete list of the available options can be obtained |
479 |
|
from:</para> |
480 |
|
|
481 |
|
<screen> |
482 |
|
$ genmake2 -help |
483 |
|
</screen> |
484 |
|
|
485 |
|
<para>The most important options for <filename>genmake2</> are:</para> |
486 |
|
|
487 |
|
<variablelist> |
488 |
|
|
489 |
|
<varlistentry> |
490 |
|
<term><filename>--optfile=/PATH/FILENAME</></term> |
491 |
|
|
492 |
|
<listitem> |
493 |
|
<para>This specifies the "options file" that should be used for a |
494 |
|
particular build. The options file is a convenient and |
495 |
|
machine-indepenent way of specifying parameters such as the |
496 |
|
FORTRAN compiler (<filename>FC=</>), FORTRAN compiler |
497 |
|
optimization flags (<filename>FFLAGS=</>), and the locations of |
498 |
|
various platform- and/or machine-specific tools |
499 |
|
(eg. <filename>MAKEDEPEND=</>). As with <filename>genmake2</>, |
500 |
|
all options files should be written to be compatible with |
501 |
|
Bourne--shell ("sh" or "BASH v1") syntax. Examples of various |
502 |
|
options files can be found in |
503 |
|
<filename>$ROOTDIR/tools/build_options</>.</para> |
504 |
|
|
505 |
|
<para>If no "optfile" is specified (either through the command lin |
506 |
|
or the environment variable), genmake2 will try to make a |
507 |
|
reasonable guess from the list provided in |
508 |
|
<filename>$ROOTDIR/tools/build_options</>. The method used for |
509 |
|
making this guess is to first determine the combination of |
510 |
|
operating system and hardware (eg. "linux_ia32") and then find a |
511 |
|
working Fortran compiler within the user's path. When these |
512 |
|
three items have been identified, genmake2 will try to find an |
513 |
|
optfile that has a matching name. </para> |
514 |
|
|
515 |
|
<para>Everyone is encouraged to submit their options files to the |
516 |
|
MITgcm project for inclusion (please send to |
517 |
|
<email>MITgcm-support@mitgcm.org</email>). We are particularly |
518 |
|
grateful for options files tested on new or unique |
519 |
|
platforms!</para> |
520 |
|
</listitem> |
521 |
|
|
522 |
|
</varlistentry> |
523 |
|
|
524 |
|
<varlistentry> |
525 |
|
<term><filename>-pdepend=/PATH/FILENAME</></term> |
526 |
|
|
527 |
|
<listitem> |
528 |
|
<para>This specifies the dependency file used for packages. If |
529 |
|
not specified, the default dependency file is |
530 |
|
<filename>$ROOTDIR/pkg/pkg_depend</>. The syntax for this file is |
531 |
|
parsed on a line-by-line basis where each line containes either a |
532 |
|
comment ("#") or a simple "PKGNAME1 (+|-)PKGNAME2" pairwise rule |
533 |
|
where the "+" or "-" symbol specifies a "must be used with" or a |
534 |
|
"must not be used with" relationship, respectively. If no rule is |
535 |
|
specified, then it is assumed that the two packages are compatible |
536 |
|
and will function either with or without each other.</para> |
537 |
|
</listitem> |
538 |
|
</varlistentry> |
539 |
|
|
540 |
|
<varlistentry> |
541 |
|
<term><filename>-pdefault=PKG</></term> |
542 |
|
<term><filename>-pdefault='PKG1 [PKG2 PKG3 ...]'</></term> |
543 |
|
<listitem> |
544 |
|
<para>This option specifies the default set of packages |
545 |
|
to be used. If not set, the default package list will |
546 |
|
be read from |
547 |
|
<filename>$ROOTDIR/pkg/pkg_default</>.</para> |
548 |
|
</listitem> |
549 |
|
</varlistentry> |
550 |
|
|
551 |
|
<varlistentry> |
552 |
|
<term><filename>-adof=/path/to/file</></term> |
553 |
|
<term><filename>-adoptfile=/path/to/file</></term> |
554 |
|
<listitem> |
555 |
|
<para>This option specifies the "adjoint" or automatic |
556 |
|
differentiation options file to be used. The file is analogous |
557 |
|
to the "optfile" defined above but it specifies information for |
558 |
|
the AD build process. The default file is located in <filename> |
559 |
|
$ROOTDIR/tools/adjoint_options/adjoint_default </> and it |
560 |
|
defines the "TAF" and "TAMC" compilers. An alternate version is |
561 |
|
also available at <filename> |
562 |
|
$ROOTDIR/tools/adjoint_options/adjoint_staf </> that selects the |
563 |
|
newer "STAF" compiler. As with any compilers, it is helpful to |
564 |
|
have their directories listed in your $PATH environment |
565 |
|
variable.</para> |
566 |
|
</listitem> |
567 |
|
</varlistentry> |
568 |
|
|
569 |
|
<varlistentry> |
570 |
|
<term><filename>-mods=DIR</></term> |
571 |
|
<term><filename>-mods='DIR1 [DIR2 ...]'</></term> |
572 |
|
<listitem> |
573 |
|
<para>This option specifies a list of directories containing |
574 |
|
"modifications". These directories contain files with names |
575 |
|
that may (or may not) exist in the main MITgcm source tree but |
576 |
|
will be overridden by any identically-named sources within the |
577 |
|
"MODS" directories. The order of precedence for this |
578 |
|
"name-hiding" is as follows:</para> |
579 |
|
|
580 |
|
<itemizedlist> |
581 |
|
<listitem><para>"MODS" directories (in the order given) |
582 |
|
</para></listitem> |
583 |
|
<listitem><para>Packages either explicitly specified or |
584 |
|
provided by default (in the order given)</para></listitem> |
585 |
|
<listitem><para>Packages included due to package dependencies |
586 |
|
(in the order that that package dependencies are |
587 |
|
parsed)</para></listitem> |
588 |
|
<listitem><para>The "standard dirs" (which may have been |
589 |
|
specified by the "-standarddirs" option)</para></listitem> |
590 |
|
</itemizedlist> |
591 |
|
|
592 |
|
</listitem> |
593 |
|
</varlistentry> |
594 |
|
|
595 |
|
<varlistentry> |
596 |
|
<term><filename>-make=/path/to/gmake</></term> |
597 |
|
<listitem> |
598 |
|
<para>Due to the poor handling of soft-links and other bugs common |
599 |
|
with the <filename>make</> versions provided by commercial Unix |
600 |
|
vendors, GNU <filename>make</filename> (sometimes called |
601 |
|
<filename>gmake</filename>) should be preferred. This option |
602 |
|
provides a means for specifying the make program to be |
603 |
|
used.</para> |
604 |
|
</listitem> |
605 |
|
</varlistentry> |
606 |
|
|
607 |
|
</variablelist> |
608 |
|
|
609 |
|
<para>A successful run of <filename>genmake2</> will produce a |
610 |
|
<filename>Makefile</>, a <filename>PACKAGES_CONFIG.h</> file, and |
611 |
|
various convenience files used for the automatic differentiation |
612 |
|
process.</para> |
613 |
|
|
614 |
|
<para>In general, it is best to use <filename>genmake2</> on a "clean" |
615 |
|
directory that is free of all source (*.[F,f],*.[F,f]90) and header |
616 |
|
(*.h,*.inc) files. Generally, this can be accomplished in an |
617 |
|
"un-clean" directory by running "make CLEAN" followed by "make |
618 |
|
makefile".</para> |
619 |
|
|
620 |
|
</sect3> |
621 |
|
|
622 |
|
<sect3 id="makefile_use"> |
623 |
|
<title>Using the <filename>Makefile</></title> |
624 |
|
|
625 |
|
<para>Once a <filename>Makefile</> has been created using |
626 |
|
<filename>genmake2</>, one can build a "standard" (forward |
627 |
|
simulator) executable using:</para> |
628 |
|
|
629 |
|
<screen> |
630 |
|
$ make CLEAN |
631 |
|
$ make depend |
632 |
|
$ make |
633 |
|
</screen> |
634 |
|
|
635 |
|
<para>The "make CLEAN" step will remove any stale source files, include |
636 |
|
files, and links. It is strongly recommended for "un-clean" |
637 |
|
directories which may contain the (perhaps partial) results of |
638 |
|
previous builds. Such "debris" can interfere with the next stage of |
639 |
|
the build.</para> |
640 |
|
|
641 |
|
<para>The "make depend" step will create a large number of symbolic |
642 |
|
links from the local directory to the source file locations. It also |
643 |
|
parses these files and creates an extensive list of dependencies |
644 |
|
within the <filename>Makefile</> itself. The links that exist at this |
645 |
|
stage are mostly "large F" files (*.F and *.F90) that need to be |
646 |
|
processed by a C preprocessor ("CPP"). Since "make depend" edits the |
647 |
|
<filename>Makefile</>, it is important not to skip this step!</para> |
648 |
|
|
649 |
|
<para>The final "make" invokes the C preprocessor to produce the "little |
650 |
|
f" files (*.f and *.f90) and then compiles them to object code using |
651 |
|
the specified FORTRAN compiler and options. An intermediate script is |
652 |
|
often used during this stage to further process (usually, make simple |
653 |
|
substitutions) custom definitions such as variable types within the |
654 |
|
source files. This additional stage is necessary in order to overcome |
655 |
|
some of the inconsistencies in the sizes of objects (bytes) between |
656 |
|
different compilers. The result of the build process is an executable |
657 |
|
with the name <filename>mitgcmuv</>.</para> |
658 |
|
|
659 |
|
<para>In addition to the forward simulator described above, the |
660 |
|
<filename>Makefile</> also has a number of targets that can be used to |
661 |
|
produce various adjoint and tangent-linear builds for optimization and |
662 |
|
other parameter-sensitivity problems. The additional targets within |
663 |
|
the <filename>Makefile</> are:</para> |
664 |
|
|
665 |
|
<variablelist> |
666 |
|
|
667 |
|
<varlistentry> |
668 |
|
<term><filename>make adall</></term> |
669 |
|
<listitem> |
670 |
|
<para>This target produces an <filename>mitgcmuv_ad</> executable |
671 |
|
using the <filename>taf</> or <filename>staf</> adjoint |
672 |
|
compiler. See the <filename>genmake2</> "-adof" option for |
673 |
|
compiler selection.</para> |
674 |
|
</listitem> |
675 |
|
</varlistentry> |
676 |
|
|
677 |
|
<varlistentry> |
678 |
|
<term><filename>make ftlall</></term> |
679 |
|
<listitem> |
680 |
|
<para>Similar to <filename>make adall</> above, this |
681 |
|
produces...</para> |
682 |
|
</listitem> |
683 |
|
</varlistentry> |
684 |
|
|
685 |
|
</variablelist> |
686 |
|
|
687 |
|
<para>Please report any compilation failures or other build problems to |
688 |
|
the <email>MITgcm-support@mitgcm.org</email> list.</para> |
689 |
|
|
690 |
|
</sect3> |
691 |
|
|
692 |
|
</sect2> |
693 |
|
|
694 |
|
<sect2 id="verification"> |
695 |
|
<title>The Verification Suite</title> |
696 |
|
|
697 |
|
<para>The MITgcm CVS tree (within the <filename>$ROOTDIR/verification/</> |
698 |
|
directory) includes more than a dozen examples intended for regression |
699 |
|
testing. Each one of these example directories contains "known-good" |
700 |
|
output files along with all the input (including both code and data |
701 |
|
files) required for their re-calculation. These example directories are |
702 |
|
further broken down into sets of subdirectories |
703 |
|
(eg. <filename>/input</>, <filename>/code</>) intended to expedite the |
704 |
|
testing process.</para> |
705 |
|
|
706 |
|
<sect3 id="testreport"> |
707 |
|
<title>The <filename>testreport</> Utility</title> |
708 |
|
|
709 |
|
<para>Also included in <filename>$ROOTDIR/verification/</> are shell |
710 |
|
scripts for automated testing. The newest script (which was written |
711 |
|
to work with <filename>genmake2</>) is called <filename>testreport</>. |
712 |
|
This script can be used to build different versions of the MITgcm |
713 |
|
code, run the various examples, compare the output, and (if specified) |
714 |
|
email the results of each one of these tests to a central |
715 |
|
repository.</para> |
716 |
|
|
717 |
|
<para>On some systems, the testreport script can be run with a command |
718 |
|
line as simple as:</para> |
719 |
|
|
720 |
|
<screen> |
721 |
|
$ cd verification |
722 |
|
$ ./testreport -ieee |
723 |
|
</screen> |
724 |
|
|
725 |
|
<para>However, some systems (those lacking or wiht a broken "/bin/sh") |
726 |
|
may require an explicit shell invocation such as:</para> |
727 |
|
|
728 |
|
<screen> |
729 |
|
$ sh ./testreport -ieee -t 'exp0 exp4' |
730 |
|
$ /some/path/to/bash ./testreport -ieee -t 'ideal_2D_oce lab_sea natl_box' |
731 |
|
</screen> |
732 |
|
|
733 |
|
<para>The <filename>testreport</> script accepts a number of |
734 |
|
command-line options which can be listed using the <filename>-help</> |
735 |
|
option. The most important ones are:</para> |
736 |
|
|
737 |
|
<variablelist> |
738 |
|
|
739 |
|
<varlistentry> |
740 |
|
<term><filename>-ieee</></term> |
741 |
|
<listitem> |
742 |
|
<para>If allowed by the compiler (as defined in the "optfile"), |
743 |
|
use IEEE arithmetic. This option, along with the GCC compiler, |
744 |
|
is how the standard results were produced.</para> |
745 |
|
</listitem> |
746 |
|
</varlistentry> |
747 |
|
|
748 |
|
<varlistentry> |
749 |
|
<term><filename>-tdir TESTDIR</></term> |
750 |
|
<term><filename>-tdir 'TDIR1 TDIR2 [...]'</></term> |
751 |
|
<listitem> |
752 |
|
<para>This option specifies the test directory or list of test |
753 |
|
directories that should be used. Each of these entries should |
754 |
|
exactly (note: they are case sensitive!) match the names of |
755 |
|
directries in <filename>$ROOTDIR/verification/</>. If this |
756 |
|
option is omitted, then all directories that are properly |
757 |
|
formatted (that is, containing an <filename>input</> |
758 |
|
sub-directory and a <filename>results/output.txt</> file) will |
759 |
|
be used.</para> |
760 |
|
</listitem> |
761 |
|
</varlistentry> |
762 |
|
|
763 |
|
<varlistentry> |
764 |
|
<term><filename>-optfile=/PATH/FILENAME</></term> |
765 |
|
<term><filename>-optfile '/PATH/F1 [/PATH/F2 ...]'</></term> |
766 |
|
<listitem> |
767 |
|
<para>This specifies a list of "options files" that will be passed |
768 |
|
to <filename>genmake2</>. If multiple options files are used |
769 |
|
(say, to test different compilers or different sets of options |
770 |
|
for the same compiler), then each options file will be used with |
771 |
|
each of the test directories.</para> |
772 |
|
</listitem> |
773 |
|
</varlistentry> |
774 |
|
|
775 |
|
<varlistentry> |
776 |
|
<term><filename>-addr EMAIL</></term> |
777 |
|
<term><filename>-addr 'EMAIL1 EMAIL2 [...]'</></term> |
778 |
|
<listitem> |
779 |
|
<para>Send the results (namely, <filename>output.txt</>, |
780 |
|
<filename>genmake_local</>, <filename>genmake_state</>, and |
781 |
|
<filename>Makefile</>) to the specified email addresses. The |
782 |
|
results are gzipped, placed in a tar file, MIME encoded, and |
783 |
|
sent to the specified address. If no email addresses are |
784 |
|
specified, no mail is sent.</para> |
785 |
|
</listitem> |
786 |
|
</varlistentry> |
787 |
|
|
788 |
|
<varlistentry> |
789 |
|
<term><filename>-mpi</></term> |
790 |
|
<listitem> |
791 |
|
<para>If the necessary files |
792 |
|
(<filename>TESTDIR/code/CPP_EEOPTIONS.h_mpi</> and |
793 |
|
<filename>TESTDIR/code/SIZE.h_mpi</>) exist, then use them for an |
794 |
|
MPI--enabled run. Note that the use of MPI typically requires a |
795 |
|
special command option (see "-command" below) to invoke the MPI |
796 |
|
executable. Examples of PBS scripts using MPI with testreport can be |
797 |
|
found in the <ulink |
798 |
|
url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/"> |
799 |
|
MITgcm-contrib area</ulink></para> |
800 |
|
</listitem> |
801 |
|
</varlistentry> |
802 |
|
|
803 |
|
<varlistentry> |
804 |
|
<term><filename>-command='some command to run'</></term> |
805 |
|
<listitem> |
806 |
|
<para>For some tests, particularly MPI runs, the default "make |
807 |
|
output.txt" is not sufficient. This option allows a more general |
808 |
|
command (or shell script) to be invoked. Examples of PBS scripts |
809 |
|
using MPI with testreport can be found in the <ulink |
810 |
|
url="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/"> |
811 |
|
MITgcm-contrib area</ulink></para> |
812 |
|
</listitem> |
813 |
|
</varlistentry> |
814 |
|
|
815 |
|
</variablelist> |
816 |
|
|
817 |
|
<para>The <filename>testreport</> script will write progress to the |
818 |
|
screen (stdout) as it runs. In addition, it will create a |
819 |
|
<filename>tr_out.txt</> file that contains a brief comparison of the |
820 |
|
current output with the "known-good" output.</para> |
821 |
|
|
822 |
|
</sect3> |
823 |
|
|
824 |
|
</sect2> |
825 |
|
|
826 |
|
|
827 |
|
<sect2 id="packages"> |
828 |
|
<title>Creating MITgcm Packages</title> |
829 |
|
|
830 |
|
<para>Optional parts of code have been separated from the MITgcmUV core |
831 |
|
driver code and organised into packages. The packaging structure |
832 |
|
provides a mechanism for maintaining suites of code, specific to |
833 |
|
particular classes of problems, in a way that is cleanly separated from |
834 |
|
the generic fluid dynamical engine.</para> |
835 |
|
|
836 |
|
<para>The MITgcmUV packaging structure is described below using generic |
837 |
|
package names ${pkg}. A concrete examples of a package is the code for |
838 |
|
implementing GM/Redi mixing. This code uses the package name</para> |
839 |
|
|
840 |
|
</sect2> |
841 |
|
|
842 |
|
</sect1> |
843 |
|
|
844 |
|
<sect1> |
845 |
|
<title>Chris's Notes...</title> |
846 |
|
|
847 |
|
<programlisting> |
848 |
|
MITgcmUV Packages |
849 |
|
================= |
850 |
|
|
851 |
|
Optional parts of code are separated from |
852 |
|
the MITgcmUV core driver code and organised into |
853 |
|
packages. The packaging structure provides a mechanism for |
854 |
|
maintaining suites of code, specific to particular |
855 |
|
classes of problem, in a way that is cleanly |
856 |
|
separated from the generic fluid dynamical engine. |
857 |
|
|
858 |
|
The MITgcmUV packaging structure is describe |
859 |
|
below using generic package names ${pkg}. |
860 |
|
A concrete examples of a package is the code |
861 |
|
for implementing GM/Redi mixing. This code uses |
862 |
|
the package name |
863 |
|
* ${PKG} = GMREDI |
864 |
|
* ${pkg} = gmredi |
865 |
|
* ${Pkg} = gmRedi |
866 |
|
|
867 |
|
Package states |
868 |
|
============== |
869 |
|
|
870 |
|
Packages can be any one of four states, included, |
871 |
|
excluded, enabled, disabled as follows: |
872 |
|
|
873 |
|
included(excluded) compile time state which |
874 |
|
includes(excludes) package |
875 |
|
code and routine calls from |
876 |
|
compilation/linking etc... |
877 |
|
|
878 |
|
enabled(disabled) run-time state which |
879 |
|
enables(disables) package code |
880 |
|
execution. |
881 |
|
|
882 |
|
Every call to a ${pkg}_... routine from outside the package |
883 |
|
should be placed within both a |
884 |
|
#ifdef ALLOW_${PKG} ... block and a |
885 |
|
if ( use${Pkg} ) ... then block. |
886 |
|
Package states are generally not expected to change during |
887 |
|
a model run. |
888 |
|
|
889 |
|
Package structure |
890 |
|
================= |
891 |
|
|
892 |
|
o Each package gets its runtime configuration |
893 |
|
parameters from a file named "data.${pkg}" |
894 |
|
Package runtime config. options are imported |
895 |
|
into a common block held in a header file |
896 |
|
called "${PKG}.h". |
897 |
|
Note: In some packages, the header file "${PKG}.h" is splitted |
898 |
|
into "${PKG}_PARAMS.h" that contains the package parameters and |
899 |
|
${PKG}_VARS.h" for the field arrays. |
900 |
|
|
901 |
|
o The core driver part of the model can check |
902 |
|
for runtime enabling or disabling of individual packages |
903 |
|
through logical flags use${Pkg}. |
904 |
|
The information is loaded from a |
905 |
|
global package setup file called "data.pkg". |
906 |
|
The use${Pkg} flags are not used within |
907 |
|
individual packages. |
908 |
|
|
909 |
|
o Included in "${PKG}.h" is a logical flag |
910 |
|
called ${Pkg}IsOn. The "${PKG}.h" header file can be imported |
911 |
|
by other packages to check dependencies and requirements |
912 |
|
from other packages ( see "Package Boot Sequence" section). |
913 |
|
NOTE: This procedure is not presently implemented, |
914 |
|
----- neither for kpp nor for gmRedi. |
915 |
|
|
916 |
|
CPP Flags |
917 |
|
========= |
918 |
|
|
919 |
|
1. Within the core driver code flags of the form |
920 |
|
ALLOW_${PKG} are used to include or exclude |
921 |
|
whole packages. The ALLOW_${PKG} flags are included |
922 |
|
from a PACKAGES_CONFIG.h file that is automatically |
923 |
|
generated by genmake2 (see genmake2 section). |
924 |
|
held in-line in the CPP_OPTIONS.h header file. |
925 |
|
e.g. |
926 |
|
|
927 |
|
Core model code ..... |
928 |
|
|
929 |
|
#include "PACKAGES_CONFIG.h" |
930 |
|
#include "CPP_OPTIONS.h" |
931 |
|
: |
932 |
|
: |
933 |
|
: |
934 |
|
|
935 |
|
#ifdef ALLOW_${PKG} |
936 |
|
if ( use${Pkg} ) CALL ${PKG}_DO_SOMETHING(...) |
937 |
|
#endif |
938 |
|
|
939 |
|
2. Within an individual package a header file, |
940 |
|
"${PKG}_OPTIONS.h", is used to set CPP flags |
941 |
|
specific to that package. It also includes |
942 |
|
"PACKAGES_CONFIG.h" and "CPP_OPTIONS.h". |
943 |
|
|
944 |
|
|
945 |
|
Package Boot Sequence |
946 |
|
===================== |
947 |
|
|
948 |
|
Calls to package routines within the core code timestepping |
949 |
|
loop can vary. However, all packages follow a required |
950 |
|
"boot" sequence outlined here: |
951 |
|
|
952 |
|
1. S/R PACKAGES_BOOT() |
953 |
|
: |
954 |
|
CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... ) |
955 |
|
|
956 |
|
|
957 |
|
2. S/R PACKAGES_READPARMS() |
958 |
|
: |
959 |
|
#ifdef ALLOW_${PKG} |
960 |
|
if ( use${Pkg} ) |
961 |
|
& CALL ${PKG}_READPARMS( retCode ) |
962 |
|
#endif |
963 |
|
|
964 |
|
3. S/R PACKAGES_INIT_FIXED() |
965 |
|
: |
966 |
|
#ifdef ALLOW_${PKG} |
967 |
|
if ( use${Pkg} ) |
968 |
|
& CALL ${PKG}_INIT_FIXED( retCode ) |
969 |
|
#endif |
970 |
|
|
971 |
|
4. S/R PACKAGES_CHECK() |
972 |
|
: |
973 |
|
#ifdef ALLOW_${PKG} |
974 |
|
if ( use${Pkg} ) |
975 |
|
& CALL ${PKG}_CHECK( retCode ) |
976 |
|
#else |
977 |
|
if ( use${Pkg} ) |
978 |
|
& CALL PACKAGES_CHECK_ERROR('${PKG}') |
979 |
|
#endif |
980 |
|
|
981 |
|
5. S/R PACKAGES_INIT_VARIABLES() |
982 |
|
: |
983 |
|
#ifdef ALLOW_${PKG} |
984 |
|
if ( use${Pkg} ) |
985 |
|
& CALL ${PKG}_INIT_VARIA( ) |
986 |
|
#endif |
987 |
|
|
988 |
|
Package Output |
989 |
|
============== |
990 |
|
6. S/R DO_THE_MODEL_IO |
991 |
|
|
992 |
|
#ifdef ALLOW_${PKG} |
993 |
|
if ( use${Pkg} ) |
994 |
|
& CALL ${PKG}_OUTPUT( ) |
995 |
|
#endif |
996 |
|
|
997 |
|
7. S/R PACKAGES_WRITE_PICKUP() |
998 |
|
|
999 |
|
#ifdef ALLOW_${PKG} |
1000 |
|
if ( use${Pkg} ) |
1001 |
|
& CALL ${PKG}_WRITE_PICKUP( ) |
1002 |
|
#endif |
1003 |
|
|
1004 |
|
Description |
1005 |
|
=========== |
1006 |
|
|
1007 |
|
- ${PKG}_READPARMS() |
1008 |
|
is responsible for reading |
1009 |
|
in the package parameters file data.${pkg}, and storing |
1010 |
|
the package parameters in "${PKG}.h" (or in "${PKG}_PARAMS.h"). |
1011 |
|
-> called from INITIALISE_FIXED in PACKAGES_READPARMS |
1012 |
|
|
1013 |
|
- ${PKG}_INIT_FIXED() |
1014 |
|
is responsible for completing the internal setup of a package. |
1015 |
|
-> called from INITIALISE_FIXED in PACKAGES_INIT_FIXED |
1016 |
|
note: 1) some pkg use instead: |
1017 |
|
CALL ${PKG}_INITIALISE ( or the old form CALL ${PKG}_INIT ) |
1018 |
|
2) for simple pkg setup, this part is done inside ${PKG}_READPARMS |
1019 |
|
|
1020 |
|
- ${PKG}_CHECK() |
1021 |
|
is responsible for validating |
1022 |
|
basic package setup and inter-package dependencies. |
1023 |
|
${PKG}_CHECK can import other package parameters it may |
1024 |
|
need to check. This is done through header files "${PKG}.h". |
1025 |
|
It is assumed that parameters owned by other packages |
1026 |
|
will not be reset during ${PKG}_CHECK(). |
1027 |
|
-> called from INITIALISE_FIXED in PACKAGES_CHECK |
1028 |
|
|
1029 |
|
- ${PKG}_INIT_VARIA() |
1030 |
|
is responsible for fill-in all package variables with an initial value. |
1031 |
|
Contains eventually a call to ${PKG}_READ_PICKUP that will read |
1032 |
|
from a pickup file the package variables required to restart the model. |
1033 |
|
This routine is called after the core model state has been completely |
1034 |
|
initialised but before the core model timestepping starts. |
1035 |
|
-> called from INITIALISE_VARIA in PACKAGES_INIT_VARIABLES |
1036 |
|
note: the name ${PKG}_INIT_VARIA is not yet standard and some pkg |
1037 |
|
use for e.g. ${PKG}_INI_VARS, ${PKG}_INIT_VARIABLES, or the old |
1038 |
|
form ${PKG}_INIT |
1039 |
|
|
1040 |
|
- ${PKG}_OUTPUT( ) |
1041 |
|
is responsible for writing time-average fields to output files |
1042 |
|
(but the cumulating step is done within the package main S/R). |
1043 |
|
Can also contain other diagnostics (.e.g. CALL ${PKG}_MONITOR) |
1044 |
|
and write snap-shot fields that are hold in common blocks. Other |
1045 |
|
temporary fields are directly dump to file where they are available. |
1046 |
|
NOTE: 1) the S/R old name ${PKG}_DIAGS is used in some packages |
1047 |
|
but is beeing replaced by ${PKG}_OUTPUT |
1048 |
|
to avoid confusion with pkg/diagnostics functionality. |
1049 |
|
2) the output part is not yet in a standard form and might still |
1050 |
|
evolve a lot. |
1051 |
|
-> called within DO_THE_MODEL_IO |
1052 |
|
|
1053 |
|
- ${PKG}_WRITE_PICKUP() |
1054 |
|
is responsible for writing a package pickup file when necessary for |
1055 |
|
a restart. (found also the old name: ${PKG}_WRITE_CHECKPOINT ) |
1056 |
|
-> called from FORWARD_STEP and THE_MODEL_MAIN in PACKAGES_WRITE_PICKUP |
1057 |
|
|
1058 |
|
Summary |
1059 |
|
======= |
1060 |
|
|
1061 |
|
- CPP options: |
1062 |
|
----------------------- |
1063 |
|
* ALLOW_${PKG} include/exclude package for compilation |
1064 |
|
|
1065 |
|
- FORTRAN logical: |
1066 |
|
----------------------- |
1067 |
|
* use${Pkg} enable package for execution at runtime |
1068 |
|
-> declared in PARAMS.h |
1069 |
|
* ${Pkg}IsOn for package cross-dependency check |
1070 |
|
-> declared in ${PKG}.h |
1071 |
|
N.B.: Not presently used! |
1072 |
|
|
1073 |
|
- header files |
1074 |
|
----------------------- |
1075 |
|
* ${PKG}_OPTIONS.h has further package-specific CPP options |
1076 |
|
* ${PKG}.h package-specific common block variables, fields |
1077 |
|
or ${PKG}_PARAMS.h package-specific common block parameters |
1078 |
|
and ${PKG}_VARS.h package-specific common block fields |
1079 |
|
|
1080 |
|
- FORTRAN source files |
1081 |
|
----------------------- |
1082 |
|
* ${pkg}_readparms.F reads parameters from file data.${pkg} |
1083 |
|
* ${pkg}_init_fixed.F complete the package setup |
1084 |
|
* ${pkg}_check.F checks package dependencies and consistencies |
1085 |
|
* ${pkg}_init_varia.F initialises package-related fields |
1086 |
|
* ${pkg}_... .F package source code |
1087 |
|
* ${pkg}_output.F write output to file. |
1088 |
|
* ${pkg}_write_pickup.F write a package pickup file to restart the model |
1089 |
|
|
1090 |
|
New: Subroutine in one package (pkgA) that only contains code which |
1091 |
|
is connected to a 2nd package (pkgB) (e.g.: gmredi_diagnostics_init.F) |
1092 |
|
will be named: pkgA_pkgB_something.F |
1093 |
|
|
1094 |
|
- parameter file |
1095 |
|
----------------------- |
1096 |
|
* data.${pkg} parameter file |
1097 |
|
</programlisting> |
1098 |
|
|
1099 |
|
</sect1> |
1100 |
|
|
1101 |
|
|
1102 |
</article> |
</article> |