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% $Header: /u/gcmpack/manual/part6/mnc.tex,v 1.6 2004/02/13 21:35:59 edhill Exp $ |
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% $Name: $ |
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\section{NetCDF I/O Integration: MNC} |
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\label{sec:pkg:mnc} |
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The \texttt{mnc} package is a set of convenience routines written to |
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expedite the process of creating, appending, and reading NetCDF files. |
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NetCDF is an increasingly popular self-describing file format |
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\cite{rew:97} intended primarily for scientific data sets. An |
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extensive collection of NetCDF reference papers, user guides, |
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software, FAQs, and other information can be obtained from UCAR's web |
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site at: |
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\begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml} |
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\begin{verbatim} |
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http://www.unidata.ucar.edu/packages/netcdf/ |
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\end{verbatim} |
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\begin{rawhtml} </A> \end{rawhtml} |
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\subsection{Introduction} |
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The \texttt{mnc} package is a two-level convenience library (or |
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``wrapper'') for most of the NetCDF Fortran API. Its purpose is to |
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streamline the user interface to NetCDF by maintaining internal |
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relations (look-up tables) keyed with strings (or names) and entities |
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such as NetCDF files, variables, and attributes. |
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The two levels of the \texttt{mnc} package are: |
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\begin{description} |
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\item[Upper level] \ |
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The upper level contains information about two kinds of |
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associations: |
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\begin{description} |
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\item[grid type] is lookup table indexed with a grid type name. |
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Each grid type name is associated with a number of dimensions, the |
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dimension sizes (one of which may be unlimited), and starting and |
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ending index arrays. The intent is to store all the necessary |
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size and shape information for the Fortran arrays containing |
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MITgcm--style ``tile'' variables (that is, a central region |
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surrounded by a variably-sized ``halo'' or exchange region as |
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shown in Figures \ref{fig:communication_primitives} and |
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\ref{fig:tiling-strategy}). |
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\item[variable type] is a lookup table indexed by a variable type |
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name. For each name, the table contains a reference to a grid |
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type for the variable and the names and values of various |
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attributes. |
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\end{description} |
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Within the upper level, these associations are not permanently tied |
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to any particular NetCDF file. This allows the information to be |
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re-used over multiple file reads and writes. |
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\item[Lower level] \ |
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In the lower (or internal) level, associations are stored for NetCDF |
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files and many of the entities that they contain including |
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dimensions, variables, and global attributes. All associations are |
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on a per-file basis. Thus, each entity is tied to a unique NetCDF |
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file and will be created or destroyed when files are, respectively, |
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opened or closed. |
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\end{description} |
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\subsection{Using MNC} |
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\subsubsection{Grid--Types and Variable--Types} |
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As a convenience for users, the MNC package includes numerous routines |
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to aid in the writing of data to NetCDF format. Probably the biggest |
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convenience is the use of pre-defined ``grid types'' and ``variable |
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types''. These ``types'' are simply look-up tables that store |
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dimensions, indicies, attributes, and other information that can all |
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be retrieved using a single character string. |
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The ``grid types'' are a way of mapping variables within MITgcm to |
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NetCDF arrays. Within MITgcm, most spatial variables are defined |
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using two-- or three--dimensional arrays with ``overlap'' regions (see |
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Figures \ref{fig:communication_primitives}, a possible vertical index, |
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and \ref{fig:tiling-strategy}) and tile indicies such as the following |
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``U'' velocity: |
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\begin{verbatim} |
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_RL uVel (1-OLx:sNx+OLx,1-OLy:sNy+OLy,Nr,nSx,nSy) |
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\end{verbatim} |
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as defined in \filelink{model/inc/DYNVARS.h}{model-inc-DYNVARS.h} |
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The grid type is a character string that encodes the presence and |
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types associated with the four possible dimensions. The character |
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string follows the format |
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\begin{center} |
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\texttt{H0\_H1\_H2\_\_V\_\_T} |
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\end{center} |
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where the terms \textit{H0}, \textit{H1}, \textit{H2}, \textit{V}, |
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\textit{T} can be almost any combination of the following: |
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\begin{center} |
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\begin{tabular}[h]{|ccc|c|c|}\hline |
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\multicolumn{3}{|c|}{Horizontal} & Vertical & Time \\ |
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\textbf{H0}: location & \textbf{H1}: dimensions & \textbf{H2}: halo |
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& \textbf{V}: location & \textbf{T}: level \\\hline |
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\texttt{-} & xy & Hn & \texttt{-} & \texttt{-} \\ |
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U & x & Hy & i & t \\ |
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V & y & & c & \\ |
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Cen & & & & \\ |
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Cor & & & & \\\hline |
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\end{tabular} |
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\end{center} |
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A example list of all pre-defined combinations is contained in the |
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file |
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\begin{center} |
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\texttt{pkg/mnc/pre-defined\_grids.txt}. |
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\end{center} |
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The variable type is an association between a variable type name and the |
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following items: |
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\begin{center} |
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\begin{tabular}[h]{|ll|}\hline |
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\textbf{Item} & \textbf{Purpose} \\\hline |
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grid type & defines the in-memory arrangement \\ |
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\texttt{bi,bj} dimensions & tiling indices, if present \\\hline |
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\end{tabular} |
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\end{center} |
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and is used by the \texttt{mnc\_cw\_*\_[R|W]} subroutines for reading |
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and writing variables. |
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\subsubsection{An Example} |
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Writing variables to NetCDF files can be accomplished in as few as two |
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function calls. The first function call defines a variable type, |
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associates it with a name (character string), and provides additional |
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information about the indicies for the tile (\texttt{bi},\texttt{bj}) |
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dimensions. The second function call will write the data at, if |
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necessary, the current time level within the model. |
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Examples of the initialization calls can be found in the file |
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\filelink{model/src/initialise\_fixed.F}{model-src-initialise_fixed.F} |
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where these four function calls: |
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{\footnotesize |
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\begin{verbatim} |
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C Create MNC definitions for DYNVARS.h variables |
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CALL MNC_CW_ADD_VNAME(myThid, 'iter', '-_-_--__-__t', 0,0) |
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CALL MNC_CW_ADD_VATTR_TEXT(myThid,'iter',1, |
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& 'long_name','iteration_count') |
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CALL MNC_CW_ADD_VNAME(myThid, 'U', 'U_xy_Hn__C__t', 4,5) |
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CALL MNC_CW_ADD_VATTR_TEXT(myThid,'U',1,'units','m/s') |
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\end{verbatim} |
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} |
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{\noindent initialize two \texttt{VNAME}s and add one NetCDF |
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attribute to each.} |
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The two variables defined above are subsequently written at specific |
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time steps within |
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\filelink{model/src/write\_state.F}{model-src-write_state.F} |
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using the function calls: |
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{\footnotesize |
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\begin{verbatim} |
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C Write the DYNVARS.h variables using the MNC package |
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mnc_iter = myIter |
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CALL MNC_CW_RL_W_R(myThid,'state',0,0,'iter',-1,mnc_iter) |
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CALL MNC_CW_RL_W_D(myThid,'state',0,0,'U', 0, uVel) |
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\end{verbatim} |
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} |
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\subsection{Key subroutines, parameters and files} |
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All of the variables used to implement the lookup tables are described |
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in \filelink{model/src/write\_state.F}{model-src-write_state.F} |
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\subsection{Package Reference} |
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