s_phys_pkgs/text/packages.tex

% $Header: /u/u3/gcmpack/manual/part6/packages.tex,v 1.2 2004/02/12 03:35:05 edhill Exp $
% $Name:  $

\section{Using MITgcm Packages}

The set of packages that will be used within a partiucular model can
be configured using a combination of both ``compile--time'' and
``run--time'' options.  Compile--time options are those used to select
which packages will be ``compiled in'' or implemented within the
program.  Packages excluded at compile time are completely absent from
the executable program(s) and thus cannot be later activated by any
set of subsequent run--time options.

\subsection{Package Inclusion/Exclusion}

There are numerous ways that one can specify compile--time package
inclusion or exclusion and they are all implemented by the
\texttt{genmake2} program which was previously described in Section
\ref{sect:buildingCode}.  The options are as follows:
\begin{enumerate}
\item Setting the \texttt{genamake2} options \texttt{--enable PKG}
  and/or \texttt{--disable PKG} specifies inclusion or exclusion.
  This method is intended as a convenient way to perform a single
  (perhaps for a quick test) compilation.
  
\item By creating a text file with the name \texttt{packages.conf} in
  either the local build directory or the \texttt{-mods=DIR}
  directory, one can specify a list of packages (one package per line,
  with '\texttt{\#}' as the comment character) to be included.  Since
  the \texttt{packages.conf} file can be saved, this is the preferred
  method for setting and recording (for future reference) the package
  configuration.
  
\item For convenience, a list of ``standard'' package groups is
  contained in the \texttt{pkg/pkg\_groups} file.  By selecting one of
  the package group names in the \texttt{packages.conf} file, one
  automatically obtains all packages in that group.

\item By default (that is, if a \texttt{packages.conf} file is not
  found), the \texttt{genmake2} program will use the contents of the
  \texttt{pkg/pkg\_default} file to obtain a list of packages.

\item To help prevent users from creating unusable package groups, the
  \texttt{genmake2} program will parse the contents of the
  \texttt{pkg/pkg\_depend} file to determine:
  \begin{itemize}
  \item whether any two requested packages cannot be simultaneously
    included (\textit{eg.} \textit{seaice} and \textit{thsice} are
    mutually exclusive),
  \item whether additional packages must be included in order to
    satisfy package dependencies (\textit{eg.} \textit{rw} depends
    upon functionality within the \textit{mdsio} package), and
  \item whether the set of all requested packages is compatible with
    the dependencies (and producing an error if they aren't).
  \end{itemize}
  Thus, as a result of the dependencies, additional packages may be
  added to those originally requested.

\end{enumerate}


\subsection{Package Activation}

For run--time package control, MITgcm uses flags set through a
\texttt{data.pkg} file.  While some packages (\textit{eg.}
\texttt{debug}, \texttt{mnc}, \texttt{exch2}) may have their own usage
conventions, most follow a simple flag naming convention of the form:
\begin{verbatim}
  usePackageName=.TRUE.
\end{verbatim}
where the \texttt{usePackageName} variable can activate or disable the
package at runtime.  As mentioned previously, packages must be
included in order to be activated.  Generally, such mistakes will be
detected and reported as errors by the code.  However, users should
still be aware of the dependency.


\section{Package Coding Standards}

The following sections describe how to modify and/or create new MITgcm
packages.

\subsection{Packages are Not Libraries}

To a beginner, the MITgcm packages may resemble libraries as used in
myriad software projects.  While future versions are likely to
implement packages as libraries (perhaps using FORTRAN90/95 syntax)
the current packages (FORTRAN77) are \textbf{not} based upon any
concept of libraries.

\subsubsection{File Inclusion Rules}

Instead, packages should be viewed only as directories containing
``sets of source files'' that are built using some simple mechanisms
provided by \texttt{genmake2}.  Conceptually, the build process adds
files as they are found and proceeds according to the following rules:
\begin{enumerate}
\item \texttt{genmake2} locates a ``core'' or main set of source files
  (the \texttt{-standarddirs} option sets these locations and the
  default value contains the directories \texttt{eesupp} and
  \texttt{model}).
  
\item \texttt{genmake2} then finds additional source files by
  inspecting the contents of each of the package directories:
  \begin{enumerate}
  \item As the new files are found, they are added to a list of source
    files.

  \item If there is a file name ``collision'' (that is, if one of the
    files in a package has the same name as one of the files
    previously encountered) then the file within the newer (more
    recently visited) package will superseed (or ``hide'') any
    previous file(s) with the same name.
    
  \item Packages are visited (and thus files discovered) {\it in the
      order that the packages are enabled} within \texttt{genmake2}.
    Thus, the files in \texttt{PackB} may superseed the files in
    \texttt{PackA} if \texttt{PackA} is enabled before \texttt{PackB}.
    Thus, package ordering can be significant!  For this reason,
    \texttt{genmake2} honors the order in which packages are
    specified.
  \end{enumerate}
\end{enumerate}

These rules were adopted since they provide a relatively simple means
for rapidly including (or ``hiding'') existing files with modified
versions.

\subsubsection{Conditional Compilation and \texttt{PACKAGES\_CONFIG.h}}

Given that packages are simply groups of files that may be added or
removed to form a whole, one may wonder how linking (that is, FORTRAN
symbol resolution) is handled.  This is the second way that
\texttt{genmake2} supports the concept of packages.  Basically,
\texttt{genmake2} creates a \texttt{Makefile} that, in turn, is able
to create a file called \texttt{PACKAGES\_CONFIG.h} that contains a set
of C pre-processor (or ``CPP'') directives such as:
\begin{verbatim}
   #undef  ALLOW_KPP
   #undef  ALLOW_LAND
   ...
   #define ALLOW_GENERIC_ADVDIFF
   #define ALLOW_MDSIO
   ...
\end{verbatim}
These CPP symbols are then used throughout the code to conditionally
isolate variable definitions, function calls, or any other code that
depends upon the presence or absence of any particular package.

An example illustrating the use of these defines is:
\begin{verbatim}
   #ifdef ALLOW_GMREDI
         IF (useGMRedi) CALL GMREDI_CALC_DIFF(
        I        bi,bj,iMin,iMax,jMin,jMax,K,
        I        maskUp,
        O        KappaRT,KappaRS,
        I        myThid)
   #endif
\end{verbatim}
which is included from the file
\filelink{calc\_diffusivity.F}{model-src-calc_diffusivity.F}
and shows how both the compile--time \texttt{ALLOW\_GMREDI} flag and the
run--time \texttt{useGMRedi} are nested.

There are some benefits to using the technique described here.  The
first is that code snippets or subroutines associated with packages
can be placed or called from almost anywhere else within the code.
The second benefit is related to memory footprint and performance.
Since unused code can be removed, there is no performance penalty due
to unnecessary memory allocation, unused function calls, or extra
run-time \texttt{IF (...)} conditions.  The major problems with this
approach are the potentially difficult-to-read and difficult-to-debug
code caused by an overuse of CPP statements.  So while it can be done,
developers should exerecise some discipline and avoid unnecesarily
``smearing'' their package implementation details across numerous
files.


\subsubsection{Package Startup or Boot Sequence}

Calls to package routines within the core code timestepping loop can
vary.  However, all packages should follow a required "boot" sequence
outlined here:

{\footnotesize
\begin{verbatim}
    1. S/R PACKAGES_BOOT()
            :
        CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... )
 

    2. S/R PACKAGES_READPARMS()
            :
        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_READPARMS( retCode )
        #endif

    3. S/R PACKAGES_INIT_FIXED()
            :
        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_INIT_FIXED( retCode )
        #endif

    4. S/R PACKAGES_CHECK()
            :
        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_CHECK( retCode )
        #else
          if ( use${Pkg} )
     &       CALL PACKAGES_CHECK_ERROR('${PKG}')
        #endif

    5. S/R PACKAGES_INIT_VARIABLES()
            :
        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_INIT_VARIA( )
        #endif

     6. S/R DO_THE_MODEL_IO

        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_DIAGS( )
        #endif

     7. S/R PACKAGES_WRITE_PICKUP()

        #ifdef ALLOW_${PKG}
          if ( use${Pkg} )
     &       CALL ${PKG}_WRITE_PICKUP( )
        #endif\end{verbatim}
}


\subsubsection{Package Startup or Boot Sequence}

1	edhill	1.3	% $Header: /u/u3/gcmpack/manual/part6/packages.tex,v 1.2 2004/02/12 03:35:05 edhill Exp $
2	edhill	1.1	% $Name: $
3
4			\section{Using MITgcm Packages}
5
6			The set of packages that will be used within a partiucular model can
7			be configured using a combination of both ``compile--time'' and
8			``run--time'' options. Compile--time options are those used to select
9			which packages will be ``compiled in'' or implemented within the
10			program. Packages excluded at compile time are completely absent from
11			the executable program(s) and thus cannot be later activated by any
12			set of subsequent run--time options.
13
14			\subsection{Package Inclusion/Exclusion}
15
16			There are numerous ways that one can specify compile--time package
17			inclusion or exclusion and they are all implemented by the
18			\texttt{genmake2} program which was previously described in Section
19			\ref{sect:buildingCode}. The options are as follows:
20			\begin{enumerate}
21			\item Setting the \texttt{genamake2} options \texttt{--enable PKG}
22			and/or \texttt{--disable PKG} specifies inclusion or exclusion.
23			This method is intended as a convenient way to perform a single
24			(perhaps for a quick test) compilation.
25
26			\item By creating a text file with the name \texttt{packages.conf} in
27			either the local build directory or the \texttt{-mods=DIR}
28			directory, one can specify a list of packages (one package per line,
29			with '\texttt{\#}' as the comment character) to be included. Since
30			the \texttt{packages.conf} file can be saved, this is the preferred
31			method for setting and recording (for future reference) the package
32			configuration.
33
34			\item For convenience, a list of ``standard'' package groups is
35			contained in the \texttt{pkg/pkg\_groups} file. By selecting one of
36			the package group names in the \texttt{packages.conf} file, one
37			automatically obtains all packages in that group.
38
39			\item By default (that is, if a \texttt{packages.conf} file is not
40			found), the \texttt{genmake2} program will use the contents of the
41			\texttt{pkg/pkg\_default} file to obtain a list of packages.
42
43			\item To help prevent users from creating unusable package groups, the
44			\texttt{genmake2} program will parse the contents of the
45			\texttt{pkg/pkg\_depend} file to determine:
46			\begin{itemize}
47			\item whether any two requested packages cannot be simultaneously
48			included (\textit{eg.} \textit{seaice} and \textit{thsice} are
49			mutually exclusive),
50			\item whether additional packages must be included in order to
51			satisfy package dependencies (\textit{eg.} \textit{rw} depends
52			upon functionality within the \textit{mdsio} package), and
53			\item whether the set of all requested packages is compatible with
54			the dependencies (and producing an error if they aren't).
55			\end{itemize}
56			Thus, as a result of the dependencies, additional packages may be
57			added to those originally requested.
58
59			\end{enumerate}
60
61
62			\subsection{Package Activation}
63
64			For run--time package control, MITgcm uses flags set through a
65			\texttt{data.pkg} file. While some packages (\textit{eg.}
66	edhill	1.2	\texttt{debug}, \texttt{mnc}, \texttt{exch2}) may have their own usage
67			conventions, most follow a simple flag naming convention of the form:
68	edhill	1.1	\begin{verbatim}
69			usePackageName=.TRUE.
70			\end{verbatim}
71			where the \texttt{usePackageName} variable can activate or disable the
72	edhill	1.2	package at runtime. As mentioned previously, packages must be
73			included in order to be activated. Generally, such mistakes will be
74			detected and reported as errors by the code. However, users should
75			still be aware of the dependency.
76	edhill	1.1
77
78	edhill	1.2	\section{Package Coding Standards}
79
80			The following sections describe how to modify and/or create new MITgcm
81			packages.
82
83			\subsection{Packages are Not Libraries}
84
85			To a beginner, the MITgcm packages may resemble libraries as used in
86			myriad software projects. While future versions are likely to
87			implement packages as libraries (perhaps using FORTRAN90/95 syntax)
88			the current packages (FORTRAN77) are \textbf{not} based upon any
89			concept of libraries.
90
91	edhill	1.3	\subsubsection{File Inclusion Rules}
92	edhill	1.2
93			Instead, packages should be viewed only as directories containing
94			``sets of source files'' that are built using some simple mechanisms
95			provided by \texttt{genmake2}. Conceptually, the build process adds
96			files as they are found and proceeds according to the following rules:
97			\begin{enumerate}
98			\item \texttt{genmake2} locates a ``core'' or main set of source files
99			(the \texttt{-standarddirs} option sets these locations and the
100			default value contains the directories \texttt{eesupp} and
101			\texttt{model}).
102
103			\item \texttt{genmake2} then finds additional source files by
104			inspecting the contents of each of the package directories:
105			\begin{enumerate}
106			\item As the new files are found, they are added to a list of source
107			files.
108
109			\item If there is a file name ``collision'' (that is, if one of the
110			files in a package has the same name as one of the files
111			previously encountered) then the file within the newer (more
112			recently visited) package will superseed (or ``hide'') any
113			previous file(s) with the same name.
114	edhill	1.3
115	edhill	1.2	\item Packages are visited (and thus files discovered) {\it in the
116			order that the packages are enabled} within \texttt{genmake2}.
117			Thus, the files in \texttt{PackB} may superseed the files in
118	edhill	1.3	\texttt{PackA} if \texttt{PackA} is enabled before \texttt{PackB}.
119			Thus, package ordering can be significant! For this reason,
120			\texttt{genmake2} honors the order in which packages are
121			specified.
122	edhill	1.2	\end{enumerate}
123			\end{enumerate}
124
125			These rules were adopted since they provide a relatively simple means
126			for rapidly including (or ``hiding'') existing files with modified
127			versions.
128
129			\subsubsection{Conditional Compilation and \texttt{PACKAGES\_CONFIG.h}}
130
131			Given that packages are simply groups of files that may be added or
132			removed to form a whole, one may wonder how linking (that is, FORTRAN
133			symbol resolution) is handled. This is the second way that
134			\texttt{genmake2} supports the concept of packages. Basically,
135			\texttt{genmake2} creates a \texttt{Makefile} that, in turn, is able
136			to create a file called \texttt{PACKAGES\_CONFIG.h} that contains a set
137			of C pre-processor (or ``CPP'') directives such as:
138			\begin{verbatim}
139			#undef ALLOW_KPP
140			#undef ALLOW_LAND
141			...
142			#define ALLOW_GENERIC_ADVDIFF
143			#define ALLOW_MDSIO
144			...
145			\end{verbatim}
146			These CPP symbols are then used throughout the code to conditionally
147			isolate variable definitions, function calls, or any other code that
148			depends upon the presence or absence of any particular package.
149
150			An example illustrating the use of these defines is:
151			\begin{verbatim}
152			#ifdef ALLOW_GMREDI
153			IF (useGMRedi) CALL GMREDI_CALC_DIFF(
154			I bi,bj,iMin,iMax,jMin,jMax,K,
155			I maskUp,
156			O KappaRT,KappaRS,
157			I myThid)
158			#endif
159			\end{verbatim}
160			which is included from the file
161			\filelink{calc\_diffusivity.F}{model-src-calc_diffusivity.F}
162	edhill	1.3	and shows how both the compile--time \texttt{ALLOW\_GMREDI} flag and the
163			run--time \texttt{useGMRedi} are nested.
164	edhill	1.2
165	edhill	1.3	There are some benefits to using the technique described here. The
166			first is that code snippets or subroutines associated with packages
167			can be placed or called from almost anywhere else within the code.
168			The second benefit is related to memory footprint and performance.
169			Since unused code can be removed, there is no performance penalty due
170			to unnecessary memory allocation, unused function calls, or extra
171			run-time \texttt{IF (...)} conditions. The major problems with this
172			approach are the potentially difficult-to-read and difficult-to-debug
173			code caused by an overuse of CPP statements. So while it can be done,
174			developers should exerecise some discipline and avoid unnecesarily
175			``smearing'' their package implementation details across numerous
176			files.
177
178
179			\subsubsection{Package Startup or Boot Sequence}
180
181			Calls to package routines within the core code timestepping loop can
182			vary. However, all packages should follow a required "boot" sequence
183			outlined here:
184	edhill	1.2
185	edhill	1.3	{\footnotesize
186			\begin{verbatim}
187			1. S/R PACKAGES_BOOT()
188			:
189			CALL OPEN_COPY_DATA_FILE( 'data.pkg', 'PACKAGES_BOOT', ... )
190
191
192			2. S/R PACKAGES_READPARMS()
193			:
194			#ifdef ALLOW_${PKG}
195			if ( use${Pkg} )
196			& CALL ${PKG}_READPARMS( retCode )
197			#endif
198
199			3. S/R PACKAGES_INIT_FIXED()
200			:
201			#ifdef ALLOW_${PKG}
202			if ( use${Pkg} )
203			& CALL ${PKG}_INIT_FIXED( retCode )
204			#endif
205
206			4. S/R PACKAGES_CHECK()
207			:
208			#ifdef ALLOW_${PKG}
209			if ( use${Pkg} )
210			& CALL ${PKG}_CHECK( retCode )
211			#else
212			if ( use${Pkg} )
213			& CALL PACKAGES_CHECK_ERROR('${PKG}')
214			#endif
215
216			5. S/R PACKAGES_INIT_VARIABLES()
217			:
218			#ifdef ALLOW_${PKG}
219			if ( use${Pkg} )
220			& CALL ${PKG}_INIT_VARIA( )
221			#endif
222
223			6. S/R DO_THE_MODEL_IO
224
225			#ifdef ALLOW_${PKG}
226			if ( use${Pkg} )
227			& CALL ${PKG}_DIAGS( )
228			#endif
229
230			7. S/R PACKAGES_WRITE_PICKUP()
231
232			#ifdef ALLOW_${PKG}
233			if ( use${Pkg} )
234			& CALL ${PKG}_WRITE_PICKUP( )
235			#endif\end{verbatim}
236			}
237	edhill	1.2
238
239	edhill	1.3	\subsubsection{Package Startup or Boot Sequence}
240	edhill	1.1