| 1 |
<!DOCTYPE ARTICLE PUBLIC "-//OASIS//DTD DocBook V4.1//EN"> |
| 2 |
|
| 3 |
<article id="MITgcm-Development-HOWTO"> |
| 4 |
|
| 5 |
<!-- |
| 6 |
Build commands: |
| 7 |
db2pdf -d ldp.dsl devel_HOWTO.sgml |
| 8 |
db2html -d ./ldp.dsl devel_HOWTO.sgml |
| 9 |
--> |
| 10 |
|
| 11 |
<articleinfo> |
| 12 |
<title>MITgcm Development HOWTO</title> |
| 13 |
|
| 14 |
<author> |
| 15 |
<firstname>Ed</firstname> |
| 16 |
<surname>Hill III</surname> |
| 17 |
<affiliation> |
| 18 |
<address><email>eh3@mit.edu</email></address> |
| 19 |
</affiliation> |
| 20 |
</author> |
| 21 |
|
| 22 |
<revhistory> |
| 23 |
<revision> |
| 24 |
<revnumber>0.01</revnumber> |
| 25 |
<date>2003-0-07</date> |
| 26 |
<authorinitials>eh3</authorinitials> |
| 27 |
<revremark> |
| 28 |
Initial version. |
| 29 |
</revremark> |
| 30 |
</revision> |
| 31 |
</revhistory> |
| 32 |
|
| 33 |
<abstract> |
| 34 |
<para>This document describes how to develop software for the |
| 35 |
MITgcm project.</para> |
| 36 |
</abstract> |
| 37 |
</articleinfo> |
| 38 |
|
| 39 |
<sect1 id="intro"> |
| 40 |
<title>Introduction</title> <para>The purpose of this document is |
| 41 |
to help new developers get "up to speed" with MITgcm |
| 42 |
development.</para> |
| 43 |
<sect2> |
| 44 |
<title>New Versions of This Document</title> <para>You can |
| 45 |
obtain the latest version of this document <ulink |
| 46 |
url="http://mitgcm.org/dev_docs/devel_HOWTO/">online</ulink> in |
| 47 |
various formats.</para> |
| 48 |
</sect2> |
| 49 |
<sect2> |
| 50 |
<title>Feedback and corrections</title> <para>If you have |
| 51 |
questions or comments about this document, please feel free to |
| 52 |
<ulink url="mailto:MITgcm-support@mitgcm.org">contact the |
| 53 |
authors</ulink>. |
| 54 |
</para> |
| 55 |
</sect2> |
| 56 |
</sect1> |
| 57 |
|
| 58 |
<sect1 id="background"> |
| 59 |
<title>Background</title> |
| 60 |
|
| 61 |
<sect2> |
| 62 |
<title>User Manual</title> |
| 63 |
|
| 64 |
<para>Before jumping into |
| 65 |
development, please familiarize yourself with the MITgcm user |
| 66 |
manual which is available <ulink |
| 67 |
url="http://mitgcm.org/">on the main web page</ulink>. This |
| 68 |
document contains volumes of useful information and is included |
| 69 |
here by reference.</para> |
| 70 |
|
| 71 |
<para>Also, a "snapshot" or<ulink |
| 72 |
url="http://mitgcm.org/dev_docs/">development version</ulink> of |
| 73 |
the user manual may be available, though this is only put on the |
| 74 |
web for testing purposes.</para> |
| 75 |
</sect2> |
| 76 |
|
| 77 |
<sect2> |
| 78 |
<title>Prerequisites</title> <para>To develop for MITgcm project |
| 79 |
you will need a UNIX or UNIX-like set of build tools including |
| 80 |
the following:</para> |
| 81 |
<blockquote> |
| 82 |
<simplelist type="inline"> |
| 83 |
<member>CVS client</member> |
| 84 |
<member>make or (preferably) GNU make</member> |
| 85 |
<member>FORTRAN compiler</member> |
| 86 |
<member>C compiler</member> |
| 87 |
<member>[ba]sh and [t]csh shells</member> |
| 88 |
<member>PERL</member> |
| 89 |
<member>LaTeX and LaTeX2HTML</member> |
| 90 |
</simplelist> |
| 91 |
</blockquote> |
| 92 |
<para>Essentially all of the work described here has been tested |
| 93 |
on recent versions of Red Hat Linux (eg. 7.3 through 9). Except |
| 94 |
where noted, all shell commands will be provided using bash |
| 95 |
syntax. |
| 96 |
</para> |
| 97 |
</sect2> |
| 98 |
|
| 99 |
</sect1> |
| 100 |
|
| 101 |
<sect1 id="cvs"> |
| 102 |
<title>CVS Repository</title> |
| 103 |
<sect2> |
| 104 |
<title>Layout</title> |
| 105 |
|
| 106 |
<para>Unlike many open source projects, the MITgcm CVS tree does |
| 107 |
not follow a simple "src", "docs", "share", and "test" directory |
| 108 |
layout. Instead, there are multiple higher-level directories |
| 109 |
that each, to some extent, depend upon the presence of the |
| 110 |
others. The tree currently resembles:</para> |
| 111 |
|
| 112 |
<programlisting>gcmpack/ |
| 113 |
MITgcm-contrib contributed code |
| 114 |
CS-regrid goes into utils |
| 115 |
cvspolicy.html -save- |
| 116 |
CVSROOT -save- |
| 117 |
development experimental stuff |
| 118 |
manual -save- |
| 119 |
misc -?- |
| 120 |
|
| 121 |
MITgcm code |
| 122 |
adjoint fold into genmake |
| 123 |
bin stub for ecco build |
| 124 |
compare01 old from 20th century |
| 125 |
diags timeave f77 in pkgs now |
| 126 |
doc tags -- connect to real docs? |
| 127 |
eesupp cnh? |
| 128 |
exe ecco user build |
| 129 |
*- jobs runtime shell scripts for |
| 130 |
| various platforms |
| 131 |
| lsopt line search |
| 132 |
m| model main dynamics (core) |
| 133 |
e| optimization_drivers ? |
| 134 |
r| optim line search interface |
| 135 |
g| pkg alternate and optional numerics, etc. |
| 136 |
e*- tools |
| 137 |
?| tutorial_examples documented tests |
| 138 |
| only populated on release1 branch |
| 139 |
| and not validated during "testscript" |
| 140 |
*- utils |
| 141 |
verification std tests |
| 142 |
|
| 143 |
|
| 144 |
mitgcmdoc -> manual -remove- |
| 145 |
mitgcm.org build web site |
| 146 |
models -?- |
| 147 |
packages -?- |
| 148 |
preprocess -?- |
| 149 |
tmp -?- |
| 150 |
</programlisting> |
| 151 |
|
| 152 |
<para>Efforts are underway to reduce the complexity.</para> |
| 153 |
|
| 154 |
</sect2> |
| 155 |
|
| 156 |
<!-- |
| 157 |
<sect2> |
| 158 |
<title>Releases</title> <para>Currently, there are two main |
| 159 |
branches:</para> |
| 160 |
<itemizedlist mark="bullet"> |
| 161 |
<listitem> |
| 162 |
<para>Development</para> |
| 163 |
<itemizedlist mark="bullet"> |
| 164 |
<listitem> |
| 165 |
<para>MAIN</para> |
| 166 |
</listitem> |
| 167 |
<listitem> |
| 168 |
<para>ecco-branch</para> |
| 169 |
</listitem> |
| 170 |
</itemizedlist> |
| 171 |
</listitem> |
| 172 |
<listitem> |
| 173 |
<para>Production</para> |
| 174 |
<itemizedlist mark="bullet"> |
| 175 |
<listitem> |
| 176 |
<para>Release1</para> |
| 177 |
</listitem> |
| 178 |
<listitem> |
| 179 |
<para>Release2</para> |
| 180 |
</listitem> |
| 181 |
</itemizedlist> |
| 182 |
</listitem> |
| 183 |
</itemizedlist> |
| 184 |
</sect2> |
| 185 |
--> |
| 186 |
|
| 187 |
<sect2> |
| 188 |
<title>Branches</title> |
| 189 |
|
| 190 |
<para>As shown in the online <ulink |
| 191 |
url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/doc/tag-index?graph=1.174">ViewCVS-generated |
| 192 |
tree</ulink>, the MITgcm codebase is split into to two branches |
| 193 |
or "lines" under which development proceeds. These two lines |
| 194 |
are referred to as the "MAIN" and "ecco" versions of the code. |
| 195 |
While not identical, the bulk of the MAIN and ecco lines are |
| 196 |
composed of files from the same codebase. |
| 197 |
</para> |
| 198 |
|
| 199 |
<para>Periodically, a "Release" branch is formed from the "MAIN" |
| 200 |
development branch. This is done in order to create a |
| 201 |
relatively stable reference point for both users and developers. |
| 202 |
The intent is that once a relese branch has been created, only |
| 203 |
bug-fixes will be added to it. Meanwhile, development (which |
| 204 |
might "break" or otherwise render invalid the documentation, |
| 205 |
tutorials, and/or examples contained within a release branch) is |
| 206 |
allowed to continue along the MAIN and ecco lines.</para> |
| 207 |
</sect2> |
| 208 |
|
| 209 |
<sect2> |
| 210 |
<title>Tagging</title> |
| 211 |
|
| 212 |
<para>The intent of tagging is to create "known-good" |
| 213 |
checkpoints that developers can use as references. |
| 214 |
Traditionally, MITgcm tagging has maintained the following |
| 215 |
conventions:</para> |
| 216 |
|
| 217 |
<orderedlist> |
| 218 |
<listitem> |
| 219 |
<para>Developer checks out code into a local CVS-managed |
| 220 |
directory, makes various changes/additions, tests these |
| 221 |
edits, and eventually reaches a point where (s)he is |
| 222 |
satisfied that the changes form a new "useful" point in the |
| 223 |
evolution of the code.</para> |
| 224 |
</listitem> |
| 225 |
|
| 226 |
<listitem> |
| 227 |
<para>The developer then runs the <ulink |
| 228 |
url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/verification/testscript">testscript</ulink> |
| 229 |
shell script to see if any problems are introduced. While |
| 230 |
not intended to be exhaustive, the test cases within the |
| 231 |
verification directory do provide some indication whether |
| 232 |
gross errors have been introduced. |
| 233 |
</para> |
| 234 |
</listitem> |
| 235 |
|
| 236 |
<listitem> |
| 237 |
<para>Having satisfied him- or herself that the changes are |
| 238 |
ready to be committed to the CVS repository, the developer |
| 239 |
then:</para> |
| 240 |
<orderedlist> |
| 241 |
<listitem> |
| 242 |
<para>adds a "checkpointXY_pre" comment (where X is a |
| 243 |
checkpoint number and Y is a letter) to the <ulink |
| 244 |
url="http://dev.mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/doc/tag-index">tag-index</ulink> |
| 245 |
file and checks it into the CVS repository</para> |
| 246 |
</listitem> |
| 247 |
<listitem> |
| 248 |
<para>submits the set of changes to the CVS repository |
| 249 |
and adds comments to <filename>tag-index</filename> |
| 250 |
describing what the changes are along with a matching |
| 251 |
"checkpointXY_post" entry</para> |
| 252 |
</listitem> |
| 253 |
</orderedlist> |
| 254 |
</listitem> |
| 255 |
</orderedlist> |
| 256 |
|
| 257 |
<para>The result of this tagging procedure is a sequence of |
| 258 |
development checkpoints with comments which resembles:</para> |
| 259 |
|
| 260 |
<programlisting> |
| 261 |
checkpoint50e_post |
| 262 |
o make KPP work with PTRACERS |
| 263 |
- fix gad_calc_rhs to call new routine kpp_transport_ptr, which is |
| 264 |
nearly a copy of kpp_transport_s |
| 265 |
- there is no analogue to SurfaceTendencyS, so I have to use |
| 266 |
gPtr(of the surface layer) instead |
| 267 |
o add a new platform SunFire+mpi (SunFire 15000) to genmake |
| 268 |
checkpoint50e_pre |
| 269 |
|
| 270 |
checkpoint50d_post |
| 271 |
o change kpp output from multiple-record state files to single-record state |
| 272 |
files analogous to write_state.F |
| 273 |
o reduce the output frequency of cg3d-related stuff to the monitor frequency, |
| 274 |
analogous to the cg2d-related output. |
| 275 |
o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, |
| 276 |
so that writing to internal file fn (with length 512) fails. |
| 277 |
checkpoint50d_pre |
| 278 |
</programlisting> |
| 279 |
|
| 280 |
<para>This information can be used to refer to various stages of |
| 281 |
the code development. For example, bugs can be traced to |
| 282 |
individual sets of CVS checkins based upon their first |
| 283 |
appearance when comparing the results from different |
| 284 |
checkpoints.</para> |
| 285 |
|
| 286 |
</sect2> |
| 287 |
</sect1> |
| 288 |
|
| 289 |
|
| 290 |
<sect1 id="documentation"> |
| 291 |
<title>Editing the Documentation</title> |
| 292 |
|
| 293 |
<sect2 id="documentation_getting"> |
| 294 |
<title>Getting the Docs and Code</title> |
| 295 |
|
| 296 |
<para>The first step towards editing the documentation is to |
| 297 |
checkout a copy of code, docs, and build scripts from the CVS |
| 298 |
server using:</para> |
| 299 |
|
| 300 |
<screen> |
| 301 |
$ export CVS_RSH=ssh |
| 302 |
$ export CVSROOT=':ext:auden.lcs.mit.edu:/u/u3/gcmpack' |
| 303 |
$ mkdir scratch |
| 304 |
$ cvs co MITgcm manual mitgcm.org |
| 305 |
</screen> |
| 306 |
|
| 307 |
<para>These commands extract the necessary information from the |
| 308 |
CVS server and create a temporary (called |
| 309 |
<filename>scratch</filename>) directory for the storage of the |
| 310 |
HTML and other files that will be created. Please note that you |
| 311 |
must either create <filename>scratch</filename> as shown or edit |
| 312 |
the various <filename>Makefile</filename>s and scripts used to |
| 313 |
create the documentation.</para> |
| 314 |
</sect2> |
| 315 |
|
| 316 |
<sect2> |
| 317 |
<title>Editing</title> |
| 318 |
|
| 319 |
<para>The documentation is contained in the |
| 320 |
<filename>manual</filename> directory in a raw LaTeX format. |
| 321 |
The main document is <filename>manual.tex</filename> and it uses |
| 322 |
<command>\input{}</command>s to include the chapters and |
| 323 |
subsections.</para> |
| 324 |
|
| 325 |
<para>Since the same LaTeX source is used to produce PostScript, |
| 326 |
PDF, and HTML output, care should be taken to follow certain |
| 327 |
conventions. Two of the most important are the usage of the |
| 328 |
<command>\filelink{}{}</command> and |
| 329 |
<command>\varlink{}{}</command> commands. Both of these |
| 330 |
commands have been defined to simplify the connection between |
| 331 |
the automatically generated ("code browser") HTML and the HTML |
| 332 |
version of the manual produced by LaTeX2HTML. They each take |
| 333 |
two arguments (corresponding to the contents of the two sets of |
| 334 |
curly braces) which are the text that the author wishes to be |
| 335 |
"wrapped" within the link, and a specially formatted link thats |
| 336 |
relative to the <filename>MITgcm</filename> directory within the |
| 337 |
CVS tree.</para> |
| 338 |
|
| 339 |
<para>The result is a command that resembles either</para> |
| 340 |
|
| 341 |
<orderedlist> |
| 342 |
<listitem> |
| 343 |
<para>a reference to a variable or subroutine name such as |
| 344 |
<command>\varlink{tRef}{tRef}</command>, or </para> |
| 345 |
</listitem> |
| 346 |
|
| 347 |
<listitem> |
| 348 |
<para>a reference to a file such as |
| 349 |
<command>\varlink{tRef}{path-to-the-file_name.F}</command> |
| 350 |
where the absolute path to the file is of the form |
| 351 |
<filename>/foo/MITgcm/path/to/the/file_name.F</filename></para> |
| 352 |
<para>(please note how the leading "/foo/MITgcm" |
| 353 |
component of the path is dropped leaving the path |
| 354 |
<emphasis>relative</emphasis> to the head of the code |
| 355 |
directory and each directory separator "/" is turned |
| 356 |
into a "-")</para> |
| 357 |
</listitem> |
| 358 |
</orderedlist> |
| 359 |
|
| 360 |
|
| 361 |
|
| 362 |
</sect2> |
| 363 |
|
| 364 |
<sect2> |
| 365 |
<title>Building</title> <para>Given the directory structure of |
| 366 |
<xref linkend="documentation_getting">, the entire documentation |
| 367 |
for the web site can be built using:</para> |
| 368 |
|
| 369 |
<screen> |
| 370 |
$ cd mitgcm.org/devel/buildweb |
| 371 |
$ make All |
| 372 |
</screen> |
| 373 |
|
| 374 |
<para>Which builds the PDF from the LaTeX source, creates the |
| 375 |
HTML output from the LaTeX source, parses the FORTRAN code base |
| 376 |
to produce a hyperlinked HTML version of the source, and then |
| 377 |
determines the cross-linking between the various HTML |
| 378 |
components.</para> |
| 379 |
|
| 380 |
<para>If there are no errors, the result of the build process |
| 381 |
(which can take 30+ minutes on a P4/2.5Ghz) will be contained |
| 382 |
within a single directory called |
| 383 |
<filename>scratch/dev_docs</filename>. This is a freshly built |
| 384 |
version of the entire on-line users manual. If you have the |
| 385 |
correct permissions, it can be directly copied to the web server |
| 386 |
area:</para> |
| 387 |
|
| 388 |
<screen> |
| 389 |
$ mv scratch/dev_docs /u/u0/httpd/html |
| 390 |
</screen> |
| 391 |
|
| 392 |
<para>and the update is complete.</para> |
| 393 |
|
| 394 |
</sect2> |
| 395 |
|
| 396 |
</sect1> |
| 397 |
|
| 398 |
|
| 399 |
|
| 400 |
</article> |
Parent Directory
| 
Revision Log
| 
Revision Graph