1 |
% $Header: /u/gcmpack/manual/s_phys_pkgs/text/packages.tex,v 1.7 2010/07/26 15:48:56 jmc Exp $ |
2 |
% $Name: $ |
3 |
|
4 |
\section{Using MITgcm Packages} |
5 |
\label{sec:pkg:using} |
6 |
\begin{rawhtml} |
7 |
<!-- CMIREDIR:package_using: --> |
8 |
\end{rawhtml} |
9 |
|
10 |
The set of packages that will be used within a partiucular model can |
11 |
be configured using a combination of both ``compile--time'' and |
12 |
``run--time'' options. Compile--time options are those used to select |
13 |
which packages will be ``compiled in'' or implemented within the |
14 |
program. Packages excluded at compile time are completely absent from |
15 |
the executable program(s) and thus cannot be later activated by any |
16 |
set of subsequent run--time options. |
17 |
|
18 |
\subsection{Package Inclusion/Exclusion} |
19 |
|
20 |
There are numerous ways that one can specify compile--time package |
21 |
inclusion or exclusion and they are all implemented by the |
22 |
\texttt{genmake2} program which was previously described in Section |
23 |
\ref{sec:buildingCode}. The options are as follows: |
24 |
\begin{enumerate} |
25 |
\item Setting the \texttt{genamake2} options \texttt{--enable PKG} |
26 |
and/or \texttt{--disable PKG} specifies inclusion or exclusion. |
27 |
This method is intended as a convenient way to perform a single |
28 |
(perhaps for a quick test) compilation. |
29 |
|
30 |
\item By creating a text file with the name \texttt{packages.conf} in |
31 |
either the local build directory or the \texttt{-mods=DIR} |
32 |
directory, one can specify a list of packages (one package per line, |
33 |
with '\texttt{\#}' as the comment character) to be included. Since |
34 |
the \texttt{packages.conf} file can be saved, this is the preferred |
35 |
method for setting and recording (for future reference) the package |
36 |
configuration. |
37 |
|
38 |
\item For convenience, a list of ``standard'' package groups is |
39 |
contained in the \texttt{pkg/pkg\_groups} file. By selecting one of |
40 |
the package group names in the \texttt{packages.conf} file, one |
41 |
automatically obtains all packages in that group. |
42 |
|
43 |
\item By default (that is, if a \texttt{packages.conf} file is not |
44 |
found), the \texttt{genmake2} program will use the |
45 |
package group default ``\texttt{default\_pkg\_list}'' as defined |
46 |
in \texttt{pkg/pkg\_groups} file. |
47 |
|
48 |
\item To help prevent users from creating unusable package groups, the |
49 |
\texttt{genmake2} program will parse the contents of the |
50 |
\texttt{pkg/pkg\_depend} file to determine: |
51 |
\begin{itemize} |
52 |
\item whether any two requested packages cannot be simultaneously |
53 |
included (\textit{eg.} \textit{seaice} and \textit{thsice} are |
54 |
mutually exclusive), |
55 |
\item whether additional packages must be included in order to |
56 |
satisfy package dependencies (\textit{eg.} \textit{rw} depends |
57 |
upon functionality within the \textit{mdsio} package), and |
58 |
\item whether the set of all requested packages is compatible with |
59 |
the dependencies (and producing an error if they aren't). |
60 |
\end{itemize} |
61 |
Thus, as a result of the dependencies, additional packages may be |
62 |
added to those originally requested. |
63 |
|
64 |
\end{enumerate} |
65 |
|
66 |
|
67 |
\subsection{Package Activation} |
68 |
|
69 |
For run--time package control, MITgcm uses flags set through a |
70 |
\texttt{data.pkg} file. While some packages (\textit{eg.} |
71 |
\texttt{debug}, \texttt{mnc}, \texttt{exch2}) may have their own usage |
72 |
conventions, most follow a simple flag naming convention of the form: |
73 |
\begin{verbatim} |
74 |
usePackageName=.TRUE. |
75 |
\end{verbatim} |
76 |
where the \texttt{usePackageName} variable can activate or disable the |
77 |
package at runtime. As mentioned previously, packages must be |
78 |
included in order to be activated. Generally, such mistakes will be |
79 |
detected and reported as errors by the code. However, users should |
80 |
still be aware of the dependency. |
81 |
|
82 |
|
83 |
\subsection{Package Coding Standards} |
84 |
|
85 |
The following sections describe how to modify and/or create new MITgcm |
86 |
packages. |
87 |
|
88 |
\subsubsection{Packages are Not Libraries} |
89 |
|
90 |
To a beginner, the MITgcm packages may resemble libraries as used in |
91 |
myriad software projects. While future versions are likely to |
92 |
implement packages as libraries (perhaps using FORTRAN90/95 syntax) |
93 |
the current packages (FORTRAN77) are \textbf{not} based upon any |
94 |
concept of libraries. |
95 |
|
96 |
\subsubsection{File Inclusion Rules} |
97 |
|
98 |
Instead, packages should be viewed only as directories containing |
99 |
``sets of source files'' that are built using some simple mechanisms |
100 |
provided by \texttt{genmake2}. Conceptually, the build process adds |
101 |
files as they are found and proceeds according to the following rules: |
102 |
\begin{enumerate} |
103 |
\item \texttt{genmake2} locates a ``core'' or main set of source files |
104 |
(the \texttt{-standarddirs} option sets these locations and the |
105 |
default value contains the directories \texttt{eesupp} and |
106 |
\texttt{model}). |
107 |
|
108 |
\item \texttt{genmake2} then finds additional source files by |
109 |
inspecting the contents of each of the package directories: |
110 |
\begin{enumerate} |
111 |
\item As the new files are found, they are added to a list of source |
112 |
files. |
113 |
|
114 |
\item If there is a file name ``collision'' (that is, if one of the |
115 |
files in a package has the same name as one of the files |
116 |
previously encountered) then the file within the newer (more |
117 |
recently visited) package will superseed (or ``hide'') any |
118 |
previous file(s) with the same name. |
119 |
|
120 |
\item Packages are visited (and thus files discovered) {\it in the |
121 |
order that the packages are enabled} within \texttt{genmake2}. |
122 |
Thus, the files in \texttt{PackB} may superseed the files in |
123 |
\texttt{PackA} if \texttt{PackA} is enabled before \texttt{PackB}. |
124 |
Thus, package ordering can be significant! For this reason, |
125 |
\texttt{genmake2} honors the order in which packages are |
126 |
specified. |
127 |
\end{enumerate} |
128 |
\end{enumerate} |
129 |
|
130 |
These rules were adopted since they provide a relatively simple means |
131 |
for rapidly including (or ``hiding'') existing files with modified |
132 |
versions. |
133 |
|
134 |
\subsubsection{Conditional Compilation and \texttt{PACKAGES\_CONFIG.h}} |
135 |
|
136 |
Given that packages are simply groups of files that may be added or |
137 |
removed to form a whole, one may wonder how linking (that is, FORTRAN |
138 |
symbol resolution) is handled. This is the second way that |
139 |
\texttt{genmake2} supports the concept of packages. Basically, |
140 |
\texttt{genmake2} creates a \texttt{Makefile} that, in turn, is able |
141 |
to create a file called \texttt{PACKAGES\_CONFIG.h} that contains a set |
142 |
of C pre-processor (or ``CPP'') directives such as: |
143 |
\begin{verbatim} |
144 |
#undef ALLOW_KPP |
145 |
#undef ALLOW_LAND |
146 |
... |
147 |
#define ALLOW_GENERIC_ADVDIFF |
148 |
#define ALLOW_MDSIO |
149 |
... |
150 |
\end{verbatim} |
151 |
These CPP symbols are then used throughout the code to conditionally |
152 |
isolate variable definitions, function calls, or any other code that |
153 |
depends upon the presence or absence of any particular package. |
154 |
|
155 |
An example illustrating the use of these defines is: |
156 |
\begin{verbatim} |
157 |
#ifdef ALLOW_GMREDI |
158 |
IF (useGMRedi) CALL GMREDI_CALC_DIFF( |
159 |
I bi,bj,iMin,iMax,jMin,jMax,K, |
160 |
I maskUp, |
161 |
O KappaRT,KappaRS, |
162 |
I myThid) |
163 |
#endif |
164 |
\end{verbatim} |
165 |
which is included from the file |
166 |
\filelink{calc\_diffusivity.F}{model-src-calc_diffusivity.F} |
167 |
and shows how both the compile--time \texttt{ALLOW\_GMREDI} flag and the |
168 |
run--time \texttt{useGMRedi} are nested. |
169 |
|
170 |
There are some benefits to using the technique described here. The |
171 |
first is that code snippets or subroutines associated with packages |
172 |
can be placed or called from almost anywhere else within the code. |
173 |
The second benefit is related to memory footprint and performance. |
174 |
Since unused code can be removed, there is no performance penalty due |
175 |
to unnecessary memory allocation, unused function calls, or extra |
176 |
run-time \texttt{IF (...)} conditions. The major problems with this |
177 |
approach are the potentially difficult-to-read and difficult-to-debug |
178 |
code caused by an overuse of CPP statements. So while it can be done, |
179 |
developers should exerecise some discipline and avoid unnecesarily |
180 |
``smearing'' their package implementation details across numerous |
181 |
files. |
182 |
|
183 |
|
184 |
\subsubsection{Package Startup or Boot Sequence} |
185 |
|
186 |
Calls to package routines within the core code timestepping loop can |
187 |
vary. However, all packages should follow a required "boot" sequence |
188 |
outlined here: |
189 |
|
190 |
{\footnotesize |
191 |
\begin{verbatim} |
192 |
1. S/R PACKAGES_BOOT() |
193 |
: |
194 |
CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... ) |
195 |
|
196 |
|
197 |
2. S/R PACKAGES_READPARMS() |
198 |
: |
199 |
#ifdef ALLOW_${PKG} |
200 |
if ( use${Pkg} ) |
201 |
& CALL ${PKG}_READPARMS( retCode ) |
202 |
#endif |
203 |
|
204 |
3. S/R PACKAGES_INIT_FIXED() |
205 |
: |
206 |
#ifdef ALLOW_${PKG} |
207 |
if ( use${Pkg} ) |
208 |
& CALL ${PKG}_INIT_FIXED( retCode ) |
209 |
#endif |
210 |
|
211 |
4. S/R PACKAGES_CHECK() |
212 |
: |
213 |
#ifdef ALLOW_${PKG} |
214 |
if ( use${Pkg} ) |
215 |
& CALL ${PKG}_CHECK( retCode ) |
216 |
#else |
217 |
if ( use${Pkg} ) |
218 |
& CALL PACKAGES_CHECK_ERROR('${PKG}') |
219 |
#endif |
220 |
|
221 |
5. S/R PACKAGES_INIT_VARIABLES() |
222 |
: |
223 |
#ifdef ALLOW_${PKG} |
224 |
if ( use${Pkg} ) |
225 |
& CALL ${PKG}_INIT_VARIA( ) |
226 |
#endif |
227 |
|
228 |
6. S/R DO_THE_MODEL_IO |
229 |
|
230 |
#ifdef ALLOW_${PKG} |
231 |
if ( use${Pkg} ) |
232 |
& CALL ${PKG}_OUTPUT( ) |
233 |
#endif |
234 |
|
235 |
7. S/R PACKAGES_WRITE_PICKUP() |
236 |
|
237 |
#ifdef ALLOW_${PKG} |
238 |
if ( use${Pkg} ) |
239 |
& CALL ${PKG}_WRITE_PICKUP( ) |
240 |
#endif\end{verbatim} |
241 |
} |
242 |
|
243 |
|
244 |
\subsubsection{Adding a package to PARAMS.h and packages\_boot()} |
245 |
|
246 |
An MITgcm package directory contains all the code needed for that package apart |
247 |
from one variable for each package. This variable is the {\it use\$\{Pkg\} } |
248 |
flag. This flag, which is of type logical, {\bf must} be declared in the |
249 |
shared header file {\it PARAMS.h} in the {\it PARM\_PACKAGES} block. This |
250 |
convention is used to support a single runtime control file {\it data.pkg} |
251 |
which is read by the startup routine {\it packages\_boot()} and that sets a |
252 |
flag controlling the runtime use of a package. This routine needs to be able to |
253 |
read the flags for packages that were not built at compile time. Therefore |
254 |
when adding a new package, in addition to creating the per-package directory |
255 |
in the {\it pkg/} subdirectory a developer should add a {\it use\$\{Pkg\} } |
256 |
flag to {\it PARAMS.h} and a {\it use\$\{Pkg\} } entry to the |
257 |
{\it packages\_boot()} {\it PACKAGES} namelist. |
258 |
The only other package specific code that should appear outside the individual |
259 |
package directory are calls to the specific package API. |
260 |
|
261 |
|