| 398 |
</sect1> |
</sect1> |
| 399 |
|
|
| 400 |
<sect1 id="coding"> |
<sect1 id="coding"> |
| 401 |
<title>Coding</title> |
<title>Coding for MITgcm</title> |
| 402 |
|
|
| 403 |
|
<sect2 id="build_tools"> |
| 404 |
|
<title>Build Tools</title> |
| 405 |
|
|
| 406 |
|
<para>Many Open Source projects use the "GNU Autotools" to help |
| 407 |
|
streamline the build process for various Unix and Unix-like |
| 408 |
|
architectures. For a user, the result is the common "configure" |
| 409 |
|
(that is, "<filename>./configure && make && make |
| 410 |
|
install</filename>") commands. For MITgcm, the process is |
| 411 |
|
similar. Typical commands are:</para> |
| 412 |
|
|
| 413 |
|
<screen> |
| 414 |
|
$ genmake -mods=../code |
| 415 |
|
$ make depend |
| 416 |
|
$ make |
| 417 |
|
</screen> |
| 418 |
|
|
| 419 |
|
<para>The following sections describe the individual steps in |
| 420 |
|
the build process.</para> |
| 421 |
|
|
| 422 |
|
<sect3 id="genmake"> |
| 423 |
|
<title>The <filename>genmake2</> Utility</title> |
| 424 |
|
|
| 425 |
|
<para><emphasis>Please note that the older |
| 426 |
|
<filename>genmake</> is deprecated and will eventually |
| 427 |
|
be replaced by <filename>genmake2</>. This HOWTO only |
| 428 |
|
describes the newer tool.</emphasis></para> |
| 429 |
|
|
| 430 |
|
<para>The first step in any MITgcm build is to create a |
| 431 |
|
Unix-style <filename>Makefile</filename> which will be parsed |
| 432 |
|
by <filename>make</filename> to specify how to compile the |
| 433 |
|
MITgcm source files. For more detailed descriptions of what |
| 434 |
|
the make tools are and how they are used, please see:</para> |
| 435 |
|
|
| 436 |
|
<itemizedlist> |
| 437 |
|
<listitem> |
| 438 |
|
<para><ulink url="http://www.gnu.org/software/make/make.html">http://www.gnu.org/software/make/make.html</></para> |
| 439 |
|
</listitem> |
| 440 |
|
<listitem> |
| 441 |
|
<para><ulink url="http://www.oreilly.com/catalog/make2/">http://www.oreilly.com/catalog/make2/</></para> |
| 442 |
|
</listitem> |
| 443 |
|
</itemizedlist> |
| 444 |
|
|
| 445 |
|
<para>Due to the poor handling of soft-links and other bugs |
| 446 |
|
common with the <filename>make</filename> versions provided by |
| 447 |
|
commercial Unix vendors, GNU <filename>make</filename> |
| 448 |
|
(sometimes called <filename>gmake</filename>) should be |
| 449 |
|
preferred.</para> |
| 450 |
|
|
| 451 |
|
<para>As the name implies, <filename>genmake2</filename> |
| 452 |
|
generates a <filename>Makefile</filename>. It does so by |
| 453 |
|
first parsing the information supplied from the following |
| 454 |
|
sources</para> |
| 455 |
|
|
| 456 |
|
<orderedlist> |
| 457 |
|
<listitem> |
| 458 |
|
<para>a <filename>gm_local</filename> file in the current |
| 459 |
|
directory</para> |
| 460 |
|
</listitem> |
| 461 |
|
<listitem> |
| 462 |
|
<para>directly from command-line options</para> |
| 463 |
|
</listitem> |
| 464 |
|
<listitem> |
| 465 |
|
<para>an "options file" as specified by the command-line |
| 466 |
|
option <filename>-optfile='FILENAME'</filename></para> |
| 467 |
|
</listitem> |
| 468 |
|
</orderedlist> |
| 469 |
|
|
| 470 |
|
<para>then checking certain dependency rules (the package |
| 471 |
|
dependencies), and then writing a |
| 472 |
|
<filename>Makefile</filename> based upon the source code that |
| 473 |
|
it finds. For convenience with the various Unix shells, |
| 474 |
|
<filename>genmake2</> supports both "long"- and "shor"-style |
| 475 |
|
options. A complete list of the available options can be |
| 476 |
|
obtained from:</para> |
| 477 |
|
|
| 478 |
|
<screen> |
| 479 |
|
$ genmake2 -help |
| 480 |
|
</screen> |
| 481 |
|
|
| 482 |
|
<para>The most important options for <filename>genmake2</> |
| 483 |
|
are:</para> |
| 484 |
|
|
| 485 |
|
<variablelist> |
| 486 |
|
|
| 487 |
|
<varlistentry> |
| 488 |
|
<term><filename>--optfile=/PATH/FILENAME</></term> |
| 489 |
|
<listitem> |
| 490 |
|
<para>This specifies the "options file" that should be |
| 491 |
|
used for a particular build. The options file is a |
| 492 |
|
convenient and machine-indepenent way of specifying |
| 493 |
|
parameters such as the FORTRAN compiler |
| 494 |
|
(<filename>FC=</>), FORTRAN compiler optimization flags |
| 495 |
|
(<filename>FFLAGS=</>), and the locations of various |
| 496 |
|
platform- and/or machine-specific tools |
| 497 |
|
(eg. <filename>MAKEDEPEND=</>). As with |
| 498 |
|
<filename>genmake2</>, all options files should be |
| 499 |
|
written a BASH v1-compatible syntax. Examples of |
| 500 |
|
various options files can be found in |
| 501 |
|
<filename>$ROOTDIR/tools/build_options</>. Everyone is |
| 502 |
|
encouraged to submit their options files to the MITgcm |
| 503 |
|
project for inclusion (please send to |
| 504 |
|
<email>MITgcm-support@mitgcm.org</email>). We are |
| 505 |
|
particularly grateful for options files tested on new or |
| 506 |
|
unique platforms!</para> |
| 507 |
|
</listitem> |
| 508 |
|
</varlistentry> |
| 509 |
|
|
| 510 |
|
<varlistentry> |
| 511 |
|
<term><filename>-pdepend=/PATH/FILENAME</></term> |
| 512 |
|
<listitem> |
| 513 |
|
<para>This specifies the dependency file used for |
| 514 |
|
packages. If not specified, the default dependency file |
| 515 |
|
is <filename>$ROOTDIR/pkg/pkg_depend</>. The syntax for |
| 516 |
|
this file is parsed on a line-by-line basis where each |
| 517 |
|
line containes either a comment ("#") or a simple |
| 518 |
|
"PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or |
| 519 |
|
"-" symbol specifies a "must be used with" or a "must |
| 520 |
|
not be used with" relationship, respectively. If no |
| 521 |
|
rule is specified, then it is assumed that the two |
| 522 |
|
packages are compatible and will function either with or |
| 523 |
|
without each other.</para> |
| 524 |
|
</listitem> |
| 525 |
|
</varlistentry> |
| 526 |
|
|
| 527 |
|
<varlistentry> |
| 528 |
|
<term><filename>-pdefault=PKG</></term> |
| 529 |
|
<term><filename>-pdefault='PKG1 [PKG2 PKG3 ...]'</></term> |
| 530 |
|
<listitem> |
| 531 |
|
<para>This option specifies the default set of packages |
| 532 |
|
to be used. If not set, the default package list will |
| 533 |
|
be read from |
| 534 |
|
<filename>$ROOTDIR/pkg/pkg_default</>.</para> |
| 535 |
|
</listitem> |
| 536 |
|
</varlistentry> |
| 537 |
|
|
| 538 |
|
<varlistentry> |
| 539 |
|
<term><filename></>-mods=DIR</term> |
| 540 |
|
<term><filename></>-mods='DIR1 [DIR2 ...]'</term> |
| 541 |
|
<listitem> |
| 542 |
|
<para>This option specifies a list of directories |
| 543 |
|
containing "modifications". These are files that may |
| 544 |
|
(or may not) exist in the main MITgcm source tree but |
| 545 |
|
will be overridden by any identically-named sources |
| 546 |
|
within the "MODS" directories.</para> |
| 547 |
|
</listitem> |
| 548 |
|
</varlistentry> |
| 549 |
|
|
| 550 |
|
</variablelist> |
| 551 |
|
|
| 552 |
|
<para>A successful run of <filename>genmake2</> will produce |
| 553 |
|
both a <filename>Makefile</> and a locally modified copy of |
| 554 |
|
the specified <filename>CPP_OPTIONS.h</> file. The local copy |
| 555 |
|
of <filename>CPP_OPTIONS.h</> will contain a list of |
| 556 |
|
<filename>genmake2</>-created #DEFINE and #UNDEF statements |
| 557 |
|
that reflect the list of packages that will be compiled into |
| 558 |
|
the code (either directly through enable/disable/defaults |
| 559 |
|
options or indirectly through dependencies).</para> |
| 560 |
|
|
| 561 |
|
<para>In general, it is best to use <filename>genmake2</> on a |
| 562 |
|
"clean" directory that is free of all source |
| 563 |
|
(*.[F,f],*.[F,f]90) and header (*.h,*.inc) files. Generally, |
| 564 |
|
this can be accomplished in an "un-clean" directory by running |
| 565 |
|
"make CLEAN" followed by "make makefile".</para> |
| 566 |
|
|
| 567 |
|
</sect3> |
| 568 |
|
|
| 569 |
|
<sect3 id="makefile_use"> |
| 570 |
|
<title>Using <filename>Makefile</></title> |
| 571 |
|
|
| 572 |
|
<para>Once a <filename>Makefile</> has been created, one can |
| 573 |
|
build the executable using:</para> |
| 574 |
|
|
| 575 |
|
<screen> |
| 576 |
|
$ make CLEAN |
| 577 |
|
$ make depend |
| 578 |
|
$ make |
| 579 |
|
</screen> |
| 580 |
|
|
| 581 |
|
<para>The "make CLEAN" step will remove any local source |
| 582 |
|
files, include files, and links. It is strongly recommended |
| 583 |
|
for "un-clean" directories which may contain the (partial?) |
| 584 |
|
results of previous builds. Such "debris" can interfere with |
| 585 |
|
the next stage of the build.</para> |
| 586 |
|
|
| 587 |
|
<para>The "make depend" step will create a large number of |
| 588 |
|
symbolic links from the local directory to the source file |
| 589 |
|
locations. It also parses these files and creates an |
| 590 |
|
extensive list of dependencies within the |
| 591 |
|
<filename>Makefile</> itself. The links that exist at this |
| 592 |
|
stage are mostly "large F" files (*.F and *.F90) that need to |
| 593 |
|
be processed by a C preprocessor ("CPP"). |
| 594 |
|
</para> |
| 595 |
|
|
| 596 |
|
<para>The final "make" invokes the C preprocessor to produce |
| 597 |
|
the "little f" files (*.f and *.f90) and then compiles them to |
| 598 |
|
object code using the specified FORTRAN compiler and options. |
| 599 |
|
An intermediate script is often used during this stage to |
| 600 |
|
further process (usually, make simple substitutions) custom |
| 601 |
|
definitions such as variable types within the source files. |
| 602 |
|
This additional stage is necessary in order to overcome some |
| 603 |
|
of the inconsistencies in the sizes of objects (bytes) between |
| 604 |
|
different compilers.</para> |
| 605 |
|
|
| 606 |
|
<para>Please report compilation failures or other problems to |
| 607 |
|
<email>MITgcm-support@mitgcm.org</email>.</para> |
| 608 |
|
|
| 609 |
|
</sect3> |
| 610 |
|
|
| 611 |
|
</sect2> |
| 612 |
|
|
| 613 |
|
<sect2 id="verification"> |
| 614 |
|
<title>The Verification Suite</title> |
| 615 |
|
|
| 616 |
|
<para>The MITgcm CVS tree (within the |
| 617 |
|
<filename>$ROOTDIR/verification/</> directory) includes more |
| 618 |
|
than a dozen examples intended for regression testing. Each one |
| 619 |
|
of these example directories contains "known-good" output files |
| 620 |
|
along with all the input (including both code and data files) |
| 621 |
|
required for their re-calculation. These example directories |
| 622 |
|
are further broken down into sets of subdirectories |
| 623 |
|
(eg. <filename>/input</>, <filename>/code</>) intended to |
| 624 |
|
expedite the testing process.</para> |
| 625 |
|
|
| 626 |
|
<sect3 id="testreport"> |
| 627 |
|
<title>The <filename>testreport</> Utility</title> |
| 628 |
|
|
| 629 |
|
<para>Also included in <filename>$ROOTDIR/verification/</> are |
| 630 |
|
shell scripts for automated testing. The newest script (which |
| 631 |
|
was written to work with <filename>genmake2</>) is called |
| 632 |
|
<filename>testreport</>. Ths script can be used to build the |
| 633 |
|
different versions of the MITgcm code, run the various |
| 634 |
|
examples, compare the output, and (if specified) email the |
| 635 |
|
results of each one of these tests to a central |
| 636 |
|
repository.</para> |
| 637 |
|
|
| 638 |
|
<para>The <filename>testreport</> script accepts a number of |
| 639 |
|
command-line options which can be listed using the |
| 640 |
|
<filename>-help</> option. The most important ones are:</para> |
| 641 |
|
|
| 642 |
|
<variablelist> |
| 643 |
|
|
| 644 |
|
<varlistentry> |
| 645 |
|
<term><filename>-tdir TESTDIR</></term> |
| 646 |
|
<term><filename>-tdir 'TDIR1 TDIR2 [...]'</></term> |
| 647 |
|
<listitem> |
| 648 |
|
<para>This option specifies the test directory or list |
| 649 |
|
of test directories that should be used. Each of these |
| 650 |
|
entries should exactly (note: they're case sensitive!) |
| 651 |
|
match the names of directries in |
| 652 |
|
<filename>$ROOTDIR/verification/</>. If this option is |
| 653 |
|
omitted, then all directories that are properly |
| 654 |
|
formatted (that is, containing an <filename>input</> |
| 655 |
|
sub-directory and example output) will be used.</para> |
| 656 |
|
</listitem> |
| 657 |
|
</varlistentry> |
| 658 |
|
|
| 659 |
|
<varlistentry> |
| 660 |
|
<term><filename>-optfile=/PATH/FILENAME</></term> |
| 661 |
|
<term><filename>-optfile '/PATH/F1 [/PATH/F2 ...]'</></term> |
| 662 |
|
<listitem> |
| 663 |
|
<para>This specifies a list of "options files" that will |
| 664 |
|
be passed to <filename>genmake2</>. If multiple options |
| 665 |
|
files are used (say, to test different compilers or |
| 666 |
|
different sets of options for the same compiler), then |
| 667 |
|
each options file will be used with each of the test |
| 668 |
|
directories.</para> |
| 669 |
|
</listitem> |
| 670 |
|
</varlistentry> |
| 671 |
|
|
| 672 |
|
<varlistentry> |
| 673 |
|
<term><filename>-addr EMAIL</></term> |
| 674 |
|
<term><filename>-addr 'EMAIL1 EMAIL2 [...]'</></term> |
| 675 |
|
<listitem> |
| 676 |
|
<para>Send the results (namely, <filename>output.txt</>, |
| 677 |
|
<filename>gm_local</>, <filename>gm_state</>, and |
| 678 |
|
<filename>Makefile</>) to the specified email addresses. |
| 679 |
|
The results are gzipped, placed in a tar file, MIME |
| 680 |
|
encoded, and sent to an @mitgcm.org address. If no |
| 681 |
|
email addresses are specified, no mail is sent.</para> |
| 682 |
|
</listitem> |
| 683 |
|
</varlistentry> |
| 684 |
|
|
| 685 |
|
</variablelist> |
| 686 |
|
|
| 687 |
|
<para>The <filename>testreport</> script will write progress |
| 688 |
|
to the screen (stdout) as it runs. In addition, it will |
| 689 |
|
create a <filename>summary.txt</> file that contains a brief |
| 690 |
|
comparison of the current output with the "known-good" |
| 691 |
|
output.</para> |
| 692 |
|
|
| 693 |
|
</sect3> |
| 694 |
|
|
| 695 |
|
</sect2> |
| 696 |
|
|
| 697 |
<sect2 id="packages"> |
<sect2 id="packages"> |
| 698 |
<title>Coding Packages</title> |
<title>Creating MITgcm Packages</title> |
| 699 |
|
|
| 700 |
<para>Optional parts of code have been separated from the MITgcmUV |
<para>Optional parts of code have been separated from the MITgcmUV |
| 701 |
core driver code and organised into packages. The packaging |
core driver code and organised into packages. The packaging |
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