--- manual/s_phys_pkgs/mnc.tex 2004/02/12 03:35:05 1.5 +++ manual/s_phys_pkgs/mnc.tex 2004/09/22 15:11:32 1.11 @@ -1,7 +1,7 @@ -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/Attic/mnc.tex,v 1.5 2004/02/12 03:35:05 edhill Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_phys_pkgs/Attic/mnc.tex,v 1.11 2004/09/22 15:11:32 edhill Exp $ % $Name: $ -\section{NetCDF I/O Integration} +\section{NetCDF I/O Integration: MNC} \label{sec:pkg:mnc} The \texttt{mnc} package is a set of convenience routines written to @@ -23,8 +23,8 @@ The \texttt{mnc} package is a two-level convenience library (or ``wrapper'') for most of the NetCDF Fortran API. Its purpose is to streamline the user interface to NetCDF by maintaining internal -relations (``look-up tables'') keyed with strings (or ``names'') and -entities such as NetCDF files, variables, and attributes. +relations (look-up tables) keyed with strings (or names) and entities +such as NetCDF files, variables, and attributes. The two levels of the \texttt{mnc} package are: \begin{description} @@ -34,7 +34,7 @@ The upper level contains information about two kinds of associations: \begin{description} - \item[Grid type] is lookup table indexed with a grid type name. + \item[grid type] is lookup table indexed with a grid type name. Each grid type name is associated with a number of dimensions, the dimension sizes (one of which may be unlimited), and starting and ending index arrays. The intent is to store all the necessary @@ -44,7 +44,7 @@ shown in Figures \ref{fig:communication_primitives} and \ref{fig:tiling-strategy}). - \item[Variable type] is a lookup table indexed by a variable type + \item[variable type] is a lookup table indexed by a variable type name. For each name, the table contains a reference to a grid type for the variable and the names and values of various attributes. @@ -68,7 +68,7 @@ \subsection{Using MNC} -\subsubsection{``Grid--Types'' and ``Variable--Types''} +\subsubsection{Grid--Types and Variable--Types} As a convenience for users, the MNC package includes numerous routines to aid in the writing of data to NetCDF format. Probably the biggest @@ -94,13 +94,13 @@ \begin{center} \texttt{H0\_H1\_H2\_\_V\_\_T} \end{center} -where the terms \textit{H0,H1,H2,V,T} can be almost any combination of -the following: +where the terms \textit{H0}, \textit{H1}, \textit{H2}, \textit{V}, +\textit{T} can be almost any combination of the following: \begin{center} \begin{tabular}[h]{|ccc|c|c|}\hline - \multicolumn{3}{|c|}{Horizontal} & Vertical & \\ - Location & Direction & Halo & Location & Time \\\hline - H0 & H1 & H2 & V & T \\\hline + \multicolumn{3}{|c|}{Horizontal} & Vertical & Time \\ + \textbf{H0}: location & \textbf{H1}: dimensions & \textbf{H2}: halo + & \textbf{V}: location & \textbf{T}: level \\\hline \texttt{-} & xy & Hn & \texttt{-} & \texttt{-} \\ U & x & Hy & i & t \\ V & y & & c & \\ @@ -114,51 +114,160 @@ \texttt{pkg/mnc/pre-defined\_grids.txt}. \end{center} +The variable type is an association between a variable type name and the +following items: +\begin{center} + \begin{tabular}[h]{|l|l|}\hline + \textbf{Item} & \textbf{Purpose} \\\hline + grid type & defines the in-memory arrangement \\ + \texttt{bi,bj} dimensions & tiling indices, if present \\\hline + \end{tabular} +\end{center} +and is used by the \texttt{mnc\_cw\_*\_[R|W]} subroutines for reading +and writing variables. + \subsubsection{An Example} Writing variables to NetCDF files can be accomplished in as few as two function calls. The first function call defines a variable type, associates it with a name (character string), and provides additional -information about the indicies for \texttt{bi,bj} dimensions. The -second function call will write variable at, if necessary, the -current time level within the model. +information about the indicies for the tile (\texttt{bi},\texttt{bj}) +dimensions. The second function call will write the data at, if +necessary, the current time level within the model. Examples of the initialization calls can be found in the file -\begin{center} - \filelink{model/src/initialise\_fixed.F}{model-src-initialise_fixed.F} -\end{center} -where these four function calls: {\footnotesize +\filelink{model/src/ini\_mnc\_io.F}{model-src-ini_mnc_io.F} +where these function calls: +{\footnotesize \begin{verbatim} - C Create MNC definitions for DYNVARS.h variables - CALL MNC_CW_ADD_VNAME(myThid, 'iter', '-_-_--__-__t', 0,0) - CALL MNC_CW_ADD_VATTR_TEXT(myThid,'iter',1, - & 'long_name','iteration_count') - CALL MNC_CW_ADD_VNAME(myThid, 'U', 'U_xy_Hn__C__t', 4,5) - CALL MNC_CW_ADD_VATTR_TEXT(myThid,'U',1,'units','m/s') -\end{verbatim} } -{\noindent initialize two \texttt{VNAME}s and add one attribute to each.} +C Create MNC definitions for DYNVARS.h variables + CALL MNC_CW_ADD_VNAME('iter', '-_-_--__-__t', 0,0, myThid) + CALL MNC_CW_ADD_VATTR_TEXT('iter',1, + & 'long_name','iteration_count', myThid) + + CALL MNC_CW_ADD_VNAME('model_time', '-_-_--__-__t', 0,0, myThid) + CALL MNC_CW_ADD_VATTR_TEXT('model_time',1, + & 'long_name','Model Time', myThid) + CALL MNC_CW_ADD_VATTR_TEXT('model_time',1,'units','s', myThid) + + CALL MNC_CW_ADD_VNAME('U', 'U_xy_Hn__C__t', 4,5, myThid) + CALL MNC_CW_ADD_VATTR_TEXT('U',1,'units','m/s', myThid) + CALL MNC_CW_ADD_VATTR_TEXT('U',1, + & 'coordinates','XU YU RC iter', myThid) + + CALL MNC_CW_ADD_VNAME('T', 'Cen_xy_Hn__C__t', 4,5, myThid) + CALL MNC_CW_ADD_VATTR_TEXT('T',1,'units','degC', myThid) + CALL MNC_CW_ADD_VATTR_TEXT('T',1,'long_name', + & 'potential_temperature', myThid) + CALL MNC_CW_ADD_VATTR_TEXT('T',1, + & 'coordinates','XC YC RC iter', myThid) +\end{verbatim} +} +{\noindent initialize four \texttt{VNAME}s and add one or more NetCDF + attributes to each.} -The two variables are subsequently written at specific time steps -within -\begin{center} - \filelink{model/src/write\_state.F}{model-src-write_state.F} -\end{center} -using the function calls: {\footnotesize +The four variables defined above are subsequently written at specific +time steps within +\filelink{model/src/write\_state.F}{model-src-write_state.F} +using the function calls: +{\footnotesize \begin{verbatim} - C Write the DYNVARS.h variables using the MNC package - mnc_iter = myIter - CALL MNC_CW_RL_W_R(myThid,'state',0,0,'iter',-1,mnc_iter) - CALL MNC_CW_RL_W_D(myThid,'state',0,0,'U', 0, uVel) -\end{verbatim} } +C Write dynvars using the MNC package + CALL MNC_CW_SET_UDIM('state', -1, myThid) + CALL MNC_CW_I_W('I','state',0,0,'iter', myIter, myThid) + CALL MNC_CW_SET_UDIM('state', 0, myThid) + CALL MNC_CW_RL_W('D','state',0,0,'model_time',myTime, myThid) + CALL MNC_CW_RL_W('D','state',0,0,'U', uVel, myThid) + CALL MNC_CW_RL_W('D','state',0,0,'T', theta, myThid) +\end{verbatim} +} -\subsection{Key subroutines, parameters and files} +\subsubsection{Parameters} -All of the variables used to implement the lookup tables are described -in \filelink{model/src/write\_state.F}{model-src-write_state.F} +Most of the MNC--related parameters are contained within a Fortran +namelist file called \texttt{data.mnc}. If this file does not exist, +then the MNC package will interpret that as an indication that it is +not to be used. If the \texttt{data.mnc} file does exist, then it may +contain the following parameters: +\begin{center} + {\footnotesize + \begin{tabular}[htb]{|l|c|l|l|}\hline + \textbf{Name} & \textbf{T} & + \textbf{Default} & \textbf{Description} \\\hline + & & & \\ + \texttt{useMNC} & L & \texttt{.FALSE.} & + \textbf{overall MNC ON/OFF switch} \\ + \texttt{mnc\_echo\_gvtypes} & L & \texttt{.FALSE.} & + echo pre-defined ``types'' (debugging) \\ + \texttt{mnc\_use\_outdir} & L & \texttt{.FALSE.} & + create a directory for output \\ + \texttt{mnc\_outdir\_str} & S & \texttt{'mnc\_'} & + output directory name \\ + \texttt{mnc\_outdir\_date} & L & \texttt{.FALSE.} & + embed date in the output dir name \\ + \texttt{pickup\_write\_mnc} & L & \texttt{.FALSE.} & + use MNC to write (create) pickup files \\ + \texttt{pickup\_read\_mnc} & L & \texttt{.FALSE.} & + use MNC to read pickup files \\ + \texttt{mnc\_use\_indir} & L & \texttt{.FALSE.} & + use a directory (path) for input \\ + \texttt{mnc\_indir\_str} & S & \texttt{''} & + input directory (or path) name \\ + \texttt{snapshot\_mnc} & L & \texttt{.FALSE.} & + write \texttt{snapshot} (instantaneous) w/MNC \\ + \texttt{monitor\_mnc} & L & \texttt{.FALSE.} & + write \texttt{monitor} w/MNC \\ + \texttt{timeave\_mnc} & L & \texttt{.FALSE.} & + write \texttt{timeave} w/MNC \\\hline + \end{tabular} + } +\end{center} +Additional MNC--related parameters are contained within the main +\texttt{data} namelist file and in some of the namelist files for +individual packages. These options are: +\begin{center} + {\footnotesize + \begin{tabular}[htb]{|l|c|l|l|}\hline + \textbf{Name} & \textbf{T} & + \textbf{Default} & \textbf{Description} \\\hline + \multicolumn{4}{|c|}{\ } \\ + \multicolumn{4}{|c|}{Main namelist file: + ``\textbf{data}''} \\\hline + \texttt{snapshot\_ioinc} & L & \texttt{.FALSE.} & + write \texttt{snapshot} ``inclusively'' \\ + \texttt{timeave\_ioinc} & L & \texttt{.FALSE.} & + write \texttt{timeave} ``inclusively'' \\ + \texttt{monitor\_ioinc} & L & \texttt{.FALSE.} & + write \texttt{monitor} ``inclusively'' \\\hline + \multicolumn{4}{|c|}{\ } \\ + \multicolumn{4}{|c|}{Diagnostics namelist file: + ``\textbf{data.diagnostics}''} \\\hline + \texttt{diag\_mnc} & L & \texttt{.FALSE.} & + write \texttt{diagnostics} w/MNC \\ + \texttt{diag\_ioinc} & L & \texttt{.FALSE.} & + write \texttt{diagnostics} ``inclusively'' \\\hline + \end{tabular} + } +\end{center} -\subsection{Package Reference} +By default, turning on MNC for a particular output stream will result +in turning off all the corresponding (usually, default) MDSIO or +STDOUT output mechanisms. In other words, output defaults to being an +exclusive selection. To enable multiple kinds of simultaneous output, +flags of the form \texttt{NAME\_ioinc} can be used where \texttt{NAME} +corresponds to the various MNC output flags. When a +\texttt{NAME\_ioinc} flag is set to \texttt{.TRUE.}, then multiple +forms of output are allowed for the \texttt{NAME} output mechanism. +The intent of this design is that typical users will only want one +kind of output while people debugging the code (particularly the I/O +routines) may want simultaneous types of output. + +This ``inclusive'' versus ``exclusive'' design is easily applied in +cases where three or more kinds of output may be generated. Thus, it +can be readily extended to additional new output types (eg. HDF5). +Input types are always exclusive.