--- manual/s_getstarted/text/getting_started.tex 2004/10/13 05:06:25 1.26 +++ manual/s_getstarted/text/getting_started.tex 2004/10/16 03:40:13 1.30 @@ -1,4 +1,4 @@ -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.26 2004/10/13 05:06:25 cnh Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.30 2004/10/16 03:40:13 edhill Exp $ % $Name: $ %\section{Getting started} @@ -15,8 +15,12 @@ this section, we provide information on how to customize the code when you are ready to try implementing the configuration you have in mind. + \section{Where to find information} \label{sect:whereToFindInfo} +\begin{rawhtml} + +\end{rawhtml} A web site is maintained for release 2 (``Pelican'') of MITgcm: \begin{rawhtml} \end{rawhtml} @@ -50,6 +54,9 @@ \section{Obtaining the code} \label{sect:obtainingCode} +\begin{rawhtml} + +\end{rawhtml} MITgcm can be downloaded from our system by following the instructions below. As a courtesy we ask that you send e-mail to us at @@ -79,7 +86,7 @@ \end{enumerate} -\subsubsection{Checkout from CVS} +\subsection{Method 1 - Checkout from CVS} \label{sect:cvs_checkout} If CVS is available on your system, we strongly encourage you to use it. CVS @@ -169,7 +176,7 @@ \end{verbatim} -\subsubsection{Conventional download method} +\subsection{Method 2 - Tar file download} \label{sect:conventionalDownload} If you do not have CVS on your system, you can download the model as a @@ -256,6 +263,9 @@ with. So please be sure you understand what you're doing. \section{Model and directory structure} +\begin{rawhtml} + +\end{rawhtml} The ``numerical'' model is contained within a execution environment support wrapper. This wrapper is designed to provide a general @@ -326,6 +336,9 @@ \section[MITgcm Example Experiments]{Example experiments} \label{sect:modelExamples} +\begin{rawhtml} + +\end{rawhtml} %% a set of twenty-four pre-configured numerical experiments @@ -486,6 +499,9 @@ \section[Building MITgcm]{Building the code} \label{sect:buildingCode} +\begin{rawhtml} + +\end{rawhtml} To compile the code, we use the {\em make} program. This uses a file ({\em Makefile}) that allows us to pre-process source files, specify @@ -507,18 +523,18 @@ % ../../../tools/genmake2 -mods=../code \end{verbatim} The command line option tells {\em genmake} to override model source -code with any files in the directory {\em ./code/}. +code with any files in the directory {\em ../code/}. On many systems, the {\em genmake2} program will be able to automatically recognize the hardware, find compilers and other tools within the user's path (``echo \$PATH''), and then choose an -appropriate set of options from the files contained in the {\em - tools/build\_options} directory. Under some circumstances, a user -may have to create a new ``optfile'' in order to specify the exact -combination of compiler, compiler flags, libraries, and other options -necessary to build a particular configuration of MITgcm. In such -cases, it is generally helpful to read the existing ``optfiles'' and -mimic their syntax. +appropriate set of options from the files (``optfiles'') contained in +the {\em tools/build\_options} directory. Under some circumstances, a +user may have to create a new ``optfile'' in order to specify the +exact combination of compiler, compiler flags, libraries, and other +options necessary to build a particular configuration of MITgcm. In +such cases, it is generally helpful to read the existing ``optfiles'' +and mimic their syntax. Through the MITgcm-support list, the MITgcm developers are willing to provide help writing or modifing ``optfiles''. And we encourage users @@ -542,7 +558,11 @@ upon which other files depend. The purpose of this is to reduce re-compilation if and when you start to modify the code. The {\tt make depend} command also creates links from the model source to this -directory. +directory. It is important to note that the {\tt make depend} stage +will occasionally produce warnings or errors since the dependency +parsing tool is unable to find all of the necessary header files +(\textit{eg.} \texttt{netcdf.inc}). In these circumstances, it is +usually OK to ignore the warnings/errors and proceed to the next step. Next compile the code: \begin{verbatim} @@ -561,404 +581,18 @@ output.txt}. -\subsection{Building/compiling the code elsewhere} - -In the example above (section \ref{sect:buildingCode}) we built the -executable in the {\em input} directory of the experiment for -convenience. You can also configure and compile the code in other -locations, for example on a scratch disk with out having to copy the -entire source tree. The only requirement to do so is you have {\tt - genmake2} in your path or you know the absolute path to {\tt - genmake2}. - -The following sections outline some possible methods of organizing -your source and data. - -\subsubsection{Building from the {\em ../code directory}} - -This is just as simple as building in the {\em input/} directory: -\begin{verbatim} -% cd verification/exp2/code -% ../../../tools/genmake2 -% make depend -% make -\end{verbatim} -However, to run the model the executable ({\em mitgcmuv}) and input -files must be in the same place. If you only have one calculation to make: -\begin{verbatim} -% cd ../input -% cp ../code/mitgcmuv ./ -% ./mitgcmuv > output.txt -\end{verbatim} -or if you will be making multiple runs with the same executable: -\begin{verbatim} -% cd ../ -% cp -r input run1 -% cp code/mitgcmuv run1 -% cd run1 -% ./mitgcmuv > output.txt -\end{verbatim} - -\subsubsection{Building from a new directory} - -Since the {\em input} directory contains input files it is often more -useful to keep {\em input} pristine and build in a new directory -within {\em verification/exp2/}: -\begin{verbatim} -% cd verification/exp2 -% mkdir build -% cd build -% ../../../tools/genmake2 -mods=../code -% make depend -% make -\end{verbatim} -This builds the code exactly as before but this time you need to copy -either the executable or the input files or both in order to run the -model. For example, -\begin{verbatim} -% cp ../input/* ./ -% ./mitgcmuv > output.txt -\end{verbatim} -or if you tend to make multiple runs with the same executable then -running in a new directory each time might be more appropriate: -\begin{verbatim} -% cd ../ -% mkdir run1 -% cp build/mitgcmuv run1/ -% cp input/* run1/ -% cd run1 -% ./mitgcmuv > output.txt -\end{verbatim} - -\subsubsection{Building on a scratch disk} - -Model object files and output data can use up large amounts of disk -space so it is often the case that you will be operating on a large -scratch disk. Assuming the model source is in {\em ~/MITgcm} then the -following commands will build the model in {\em /scratch/exp2-run1}: -\begin{verbatim} -% cd /scratch/exp2-run1 -% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ - -mods=~/MITgcm/verification/exp2/code -% make depend -% make -\end{verbatim} -To run the model here, you'll need the input files: -\begin{verbatim} -% cp ~/MITgcm/verification/exp2/input/* ./ -% ./mitgcmuv > output.txt -\end{verbatim} - -As before, you could build in one directory and make multiple runs of -the one experiment: -\begin{verbatim} -% cd /scratch/exp2 -% mkdir build -% cd build -% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ - -mods=~/MITgcm/verification/exp2/code -% make depend -% make -% cd ../ -% cp -r ~/MITgcm/verification/exp2/input run2 -% cd run2 -% ./mitgcmuv > output.txt -\end{verbatim} - - -\subsection{Using \texttt{genmake2}} -\label{sect:genmake} - -To compile the code, first use the program \texttt{genmake2} (located -in the \texttt{tools} directory) to generate a Makefile. -\texttt{genmake2} is a shell script written to work with all -``sh''--compatible shells including bash v1, bash v2, and Bourne. -Internally, \texttt{genmake2} determines the locations of needed -files, the compiler, compiler options, libraries, and Unix tools. It -relies upon a number of ``optfiles'' located in the -\texttt{tools/build\_options} directory. - -The purpose of the optfiles is to provide all the compilation options -for particular ``platforms'' (where ``platform'' roughly means the -combination of the hardware and the compiler) and code configurations. -Given the combinations of possible compilers and library dependencies -({\it eg.} MPI and NetCDF) there may be numerous optfiles available -for a single machine. The naming scheme for the majority of the -optfiles shipped with the code is -\begin{center} - {\bf OS\_HARDWARE\_COMPILER } -\end{center} -where -\begin{description} -\item[OS] is the name of the operating system (generally the - lower-case output of the {\tt 'uname'} command) -\item[HARDWARE] is a string that describes the CPU type and - corresponds to output from the {\tt 'uname -m'} command: - \begin{description} - \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686, - and athlon - \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2) - \item[amd64] is AMD x86\_64 systems - \item[ppc] is for Mac PowerPC systems - \end{description} -\item[COMPILER] is the compiler name (generally, the name of the - FORTRAN executable) -\end{description} - -In many cases, the default optfiles are sufficient and will result in -usable Makefiles. However, for some machines or code configurations, -new ``optfiles'' must be written. To create a new optfile, it is -generally best to start with one of the defaults and modify it to suit -your needs. Like \texttt{genmake2}, the optfiles are all written -using a simple ``sh''--compatible syntax. While nearly all variables -used within \texttt{genmake2} may be specified in the optfiles, the -critical ones that should be defined are: - -\begin{description} -\item[FC] the FORTRAN compiler (executable) to use -\item[DEFINES] the command-line DEFINE options passed to the compiler -\item[CPP] the C pre-processor to use -\item[NOOPTFLAGS] options flags for special files that should not be - optimized -\end{description} - -For example, the optfile for a typical Red Hat Linux machine (``ia32'' -architecture) using the GCC (g77) compiler is -\begin{verbatim} -FC=g77 -DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4' -CPP='cpp -traditional -P' -NOOPTFLAGS='-O0' -# For IEEE, use the "-ffloat-store" option -if test "x$IEEE" = x ; then - FFLAGS='-Wimplicit -Wunused -Wuninitialized' - FOPTIM='-O3 -malign-double -funroll-loops' -else - FFLAGS='-Wimplicit -Wunused -ffloat-store' - FOPTIM='-O0 -malign-double' -fi -\end{verbatim} - -If you write an optfile for an unrepresented machine or compiler, you -are strongly encouraged to submit the optfile to the MITgcm project -for inclusion. Please send the file to the -\begin{rawhtml} \end{rawhtml} -\begin{center} - MITgcm-support@mitgcm.org -\end{center} -\begin{rawhtml} \end{rawhtml} -mailing list. - -In addition to the optfiles, \texttt{genmake2} supports a number of -helpful command-line options. A complete list of these options can be -obtained from: -\begin{verbatim} -% genmake2 -h -\end{verbatim} - -The most important command-line options are: -\begin{description} - -\item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that - should be used for a particular build. - - If no "optfile" is specified (either through the command line or the - MITGCM\_OPTFILE environment variable), genmake2 will try to make a - reasonable guess from the list provided in {\em - tools/build\_options}. The method used for making this guess is - to first determine the combination of operating system and hardware - (eg. "linux\_ia32") and then find a working FORTRAN compiler within - the user's path. When these three items have been identified, - genmake2 will try to find an optfile that has a matching name. - -\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default - set of packages to be used. The normal order of precedence for - packages is as follows: - \begin{enumerate} - \item If available, the command line (\texttt{--pdefault}) settings - over-rule any others. - - \item Next, \texttt{genmake2} will look for a file named - ``\texttt{packages.conf}'' in the local directory or in any of the - directories specified with the \texttt{--mods} option. - - \item Finally, if neither of the above are available, - \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file. - \end{enumerate} - -\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file - used for packages. - - If not specified, the default dependency file {\em pkg/pkg\_depend} - is used. The syntax for this file is parsed on a line-by-line basis - where each line containes either a comment ("\#") or a simple - "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol - specifies a "must be used with" or a "must not be used with" - relationship, respectively. If no rule is specified, then it is - assumed that the two packages are compatible and will function - either with or without each other. - -\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or - automatic differentiation options file to be used. The file is - analogous to the ``optfile'' defined above but it specifies - information for the AD build process. - - The default file is located in {\em - tools/adjoint\_options/adjoint\_default} and it defines the "TAF" - and "TAMC" compilers. An alternate version is also available at - {\em tools/adjoint\_options/adjoint\_staf} that selects the newer - "STAF" compiler. As with any compilers, it is helpful to have their - directories listed in your {\tt \$PATH} environment variable. - -\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of - directories containing ``modifications''. These directories contain - files with names that may (or may not) exist in the main MITgcm - source tree but will be overridden by any identically-named sources - within the ``MODS'' directories. - - The order of precedence for this "name-hiding" is as follows: - \begin{itemize} - \item ``MODS'' directories (in the order given) - \item Packages either explicitly specified or provided by default - (in the order given) - \item Packages included due to package dependencies (in the order - that that package dependencies are parsed) - \item The "standard dirs" (which may have been specified by the - ``-standarddirs'' option) - \end{itemize} - -\item[\texttt{--mpi}] This option enables certain MPI features (using - CPP \texttt{\#define}s) within the code and is necessary for MPI - builds (see Section \ref{sect:mpi-build}). - -\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of - soft-links and other bugs common with the \texttt{make} versions - provided by commercial Unix vendors, GNU \texttt{make} (sometimes - called \texttt{gmake}) should be preferred. This option provides a - means for specifying the make executable to be used. - -\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX) - machines, the ``bash'' shell is unavailable. To run on these - systems, \texttt{genmake2} can be invoked using an ``sh'' (that is, - a Bourne, POSIX, or compatible) shell. The syntax in these - circumstances is: - \begin{center} - \texttt{\% /bin/sh genmake2 -bash=/bin/sh [...options...]} - \end{center} - where \texttt{/bin/sh} can be replaced with the full path and name - of the desired shell. - -\end{description} - - -\subsection{Building with MPI} -\label{sect:mpi-build} - -Building MITgcm to use MPI libraries can be complicated due to the -variety of different MPI implementations available, their dependencies -or interactions with different compilers, and their often ad-hoc -locations within file systems. For these reasons, its generally a -good idea to start by finding and reading the documentation for your -machine(s) and, if necessary, seeking help from your local systems -administrator. - -The steps for building MITgcm with MPI support are: -\begin{enumerate} - -\item Determine the locations of your MPI-enabled compiler and/or MPI - libraries and put them into an options file as described in Section - \ref{sect:genmake}. One can start with one of the examples in: - \begin{rawhtml} - \end{rawhtml} - \begin{center} - \texttt{MITgcm/tools/build\_options/} - \end{center} - \begin{rawhtml} \end{rawhtml} - such as \texttt{linux\_ia32\_g77+mpi\_cg01} or - \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at - hand. You may need help from your user guide or local systems - administrator to determine the exact location of the MPI libraries. - If libraries are not installed, MPI implementations and related - tools are available including: - \begin{itemize} - \item \begin{rawhtml} - \end{rawhtml} - MPICH - \begin{rawhtml} \end{rawhtml} - - \item \begin{rawhtml} - \end{rawhtml} - LAM/MPI - \begin{rawhtml} \end{rawhtml} - - \item \begin{rawhtml} - \end{rawhtml} - MPIexec - \begin{rawhtml} \end{rawhtml} - \end{itemize} - -\item Build the code with the \texttt{genmake2} \texttt{-mpi} option - (see Section \ref{sect:genmake}) using commands such as: -{\footnotesize \begin{verbatim} - % ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE - % make depend - % make -\end{verbatim} } - -\item Run the code with the appropriate MPI ``run'' or ``exec'' - program provided with your particular implementation of MPI. - Typical MPI packages such as MPICH will use something like: -\begin{verbatim} - % mpirun -np 4 -machinefile mf ./mitgcmuv -\end{verbatim} - Sightly more complicated scripts may be needed for many machines - since execution of the code may be controlled by both the MPI - library and a job scheduling and queueing system such as PBS, - LoadLeveller, Condor, or any of a number of similar tools. A few - example scripts (those used for our \begin{rawhtml} \end{rawhtml}regular - verification runs\begin{rawhtml} \end{rawhtml}) are available - at: - \begin{rawhtml} - \end{rawhtml} - {\footnotesize \tt - http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ } - \begin{rawhtml} \end{rawhtml} - -\end{enumerate} - -An example of the above process on the MITgcm cluster (``cg01'') using -the GNU g77 compiler and the mpich MPI library is: - -{\footnotesize \begin{verbatim} - % cd MITgcm/verification/exp5 - % mkdir build - % cd build - % ../../../tools/genmake2 -mpi -mods=../code \ - -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01 - % make depend - % make - % cd ../input - % /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \ - -machinefile mf --gm-kill 5 -v -np 2 ../build/mitgcmuv -\end{verbatim} } - - - \section[Running MITgcm]{Running the model in prognostic mode} \label{sect:runModel} +\begin{rawhtml} + +\end{rawhtml} If compilation finished succesfuully (section \ref{sect:buildingCode}) then an executable called \texttt{mitgcmuv} will now exist in the local directory. -To run the model as a single process (ie. not in parallel) simply -type: +To run the model as a single process (\textit{ie.} not in parallel) +simply type: \begin{verbatim} % ./mitgcmuv \end{verbatim} @@ -972,17 +606,30 @@ \begin{verbatim} % ./mitgcmuv > output.txt \end{verbatim} +In the event that the model encounters an error and stops, it is very +helpful to include the last few line of this \texttt{output.txt} file +along with the (\texttt{stderr}) error message within any bug reports. For the example experiments in {\em verification}, an example of the -output is kept in {\em results/output.txt} for comparison. You can compare -your {\em output.txt} with this one to check that the set-up works. +output is kept in {\em results/output.txt} for comparison. You can +compare your {\em output.txt} with the corresponding one for that +experiment to check that the set-up works. \subsection{Output files} -The model produces various output files. At a minimum, the instantaneous -``state'' of the model is written out, which is made of the following files: +The model produces various output files. Depending upon the I/O +package selected (either \texttt{mdsio} or \texttt{mnc} or both as +determined by both the compile-time settings and the run-time flags in +\texttt{data.pkg}), the following output may appear. + + +\subsubsection{MDSIO output files} + +The ``traditional'' output files are generated by the \texttt{mdsio} +package. At a minimum, the instantaneous ``state'' of the model is +written out, which is made of the following files: \begin{itemize} \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $> @@ -1030,19 +677,58 @@ used to restart the model but are overwritten every other time they are output to save disk space during long integrations. + + +\subsubsection{MNC output files} + +Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output +is usually (though not necessarily) placed within a subdirectory with +a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}. The files +within this subdirectory are all in the ``self-describing'' netCDF +format and can thus be browsed and/or plotted using tools such as: +\begin{itemize} +\item At a minimum, the \texttt{ncdump} utility is typically included + with every netCDF install: + \begin{rawhtml} \end{rawhtml} +\begin{verbatim} +http://www.unidata.ucar.edu/packages/netcdf/ +\end{verbatim} + \begin{rawhtml} \end{rawhtml} + +\item The \texttt{ncview} utility is a very convenient and quick way + to plot netCDF data and it runs on most OSes: + \begin{rawhtml} \end{rawhtml} +\begin{verbatim} +http://meteora.ucsd.edu/~pierce/ncview_home_page.html +\end{verbatim} + \begin{rawhtml} \end{rawhtml} + +\item MatLAB(c) and other common post-processing environments provide + various netCDF interfaces including: + \begin{rawhtml} \end{rawhtml} +\begin{verbatim} +http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html +\end{verbatim} + \begin{rawhtml} \end{rawhtml} + +\end{itemize} + + \subsection{Looking at the output} -All the model data are written according to a ``meta/data'' file format. -Each variable is associated with two files with suffix names \textit{.data} -and \textit{.meta}. The \textit{.data} file contains the data written in -binary form (big\_endian by default). The \textit{.meta} file is a -``header'' file that contains information about the size and the structure -of the \textit{.data} file. This way of organizing the output is -particularly useful when running multi-processors calculations. The base -version of the model includes a few matlab utilities to read output files -written in this format. The matlab scripts are located in the directory -\textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads -the data. Look at the comments inside the script to see how to use it. +The ``traditional'' or mdsio model data are written according to a +``meta/data'' file format. Each variable is associated with two files +with suffix names \textit{.data} and \textit{.meta}. The +\textit{.data} file contains the data written in binary form +(big\_endian by default). The \textit{.meta} file is a ``header'' file +that contains information about the size and the structure of the +\textit{.data} file. This way of organizing the output is particularly +useful when running multi-processors calculations. The base version of +the model includes a few matlab utilities to read output files written +in this format. The matlab scripts are located in the directory +\textit{utils/matlab} under the root tree. The script \textit{rdmds.m} +reads the data. Look at the comments inside the script to see how to +use it. Some examples of reading and visualizing some output in {\em Matlab}: \begin{verbatim} @@ -1059,422 +745,4 @@ >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end \end{verbatim} -\section[Customizing MITgcm]{Doing it yourself: customizing the code} - -When you are ready to run the model in the configuration you want, the -easiest thing is to use and adapt the setup of the case studies -experiment (described previously) that is the closest to your -configuration. Then, the amount of setup will be minimized. In this -section, we focus on the setup relative to the ``numerical model'' -part of the code (the setup relative to the ``execution environment'' -part is covered in the parallel implementation section) and on the -variables and parameters that you are likely to change. - -\subsection{Configuration and setup} - -The CPP keys relative to the ``numerical model'' part of the code are -all defined and set in the file \textit{CPP\_OPTIONS.h }in the -directory \textit{ model/inc }or in one of the \textit{code -}directories of the case study experiments under -\textit{verification.} The model parameters are defined and declared -in the file \textit{model/inc/PARAMS.h }and their default values are -set in the routine \textit{model/src/set\_defaults.F. }The default -values can be modified in the namelist file \textit{data }which needs -to be located in the directory where you will run the model. The -parameters are initialized in the routine -\textit{model/src/ini\_parms.F}. Look at this routine to see in what -part of the namelist the parameters are located. - -In what follows the parameters are grouped into categories related to -the computational domain, the equations solved in the model, and the -simulation controls. - -\subsection{Computational domain, geometry and time-discretization} - -\begin{description} -\item[dimensions] \ - - The number of points in the x, y, and r directions are represented - by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr} - respectively which are declared and set in the file - \textit{model/inc/SIZE.h}. (Again, this assumes a mono-processor - calculation. For multiprocessor calculations see the section on - parallel implementation.) - -\item[grid] \ - - Three different grids are available: cartesian, spherical polar, and - curvilinear (which includes the cubed sphere). The grid is set - through the logical variables \textbf{usingCartesianGrid}, - \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}. - In the case of spherical and curvilinear grids, the southern - boundary is defined through the variable \textbf{phiMin} which - corresponds to the latitude of the southern most cell face (in - degrees). The resolution along the x and y directions is controlled - by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the - case of a cartesian grid, in degrees otherwise). The vertical grid - spacing is set through the 1D array \textbf{delz} for the ocean (in - meters) or \textbf{delp} for the atmosphere (in Pa). The variable - \textbf{Ro\_SeaLevel} represents the standard position of Sea-Level - in ``R'' coordinate. This is typically set to 0m for the ocean - (default value) and 10$^{5}$Pa for the atmosphere. For the - atmosphere, also set the logical variable \textbf{groundAtK1} to - \texttt{'.TRUE.'} which puts the first level (k=1) at the lower - boundary (ground). - - For the cartesian grid case, the Coriolis parameter $f$ is set - through the variables \textbf{f0} and \textbf{beta} which correspond - to the reference Coriolis parameter (in s$^{-1}$) and - $\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively. - If \textbf{beta } is set to a nonzero value, \textbf{f0} is the - value of $f$ at the southern edge of the domain. - -\item[topography - full and partial cells] \ - - The domain bathymetry is read from a file that contains a 2D (x,y) - map of depths (in m) for the ocean or pressures (in Pa) for the - atmosphere. The file name is represented by the variable - \textbf{bathyFile}. The file is assumed to contain binary numbers - giving the depth (pressure) of the model at each grid cell, ordered - with the x coordinate varying fastest. The points are ordered from - low coordinate to high coordinate for both axes. The model code - applies without modification to enclosed, periodic, and double - periodic domains. Periodicity is assumed by default and is - suppressed by setting the depths to 0m for the cells at the limits - of the computational domain (note: not sure this is the case for the - atmosphere). The precision with which to read the binary data is - controlled by the integer variable \textbf{readBinaryPrec} which can - take the value \texttt{32} (single precision) or \texttt{64} (double - precision). See the matlab program \textit{gendata.m} in the - \textit{input} directories under \textit{verification} to see how - the bathymetry files are generated for the case study experiments. - - To use the partial cell capability, the variable \textbf{hFacMin} - needs to be set to a value between 0 and 1 (it is set to 1 by - default) corresponding to the minimum fractional size of the cell. - For example if the bottom cell is 500m thick and \textbf{hFacMin} is - set to 0.1, the actual thickness of the cell (i.e. used in the code) - can cover a range of discrete values 50m apart from 50m to 500m - depending on the value of the bottom depth (in \textbf{bathyFile}) - at this point. - - Note that the bottom depths (or pressures) need not coincide with - the models levels as deduced from \textbf{delz} or \textbf{delp}. - The model will interpolate the numbers in \textbf{bathyFile} so that - they match the levels obtained from \textbf{delz} or \textbf{delp} - and \textbf{hFacMin}. - - (Note: the atmospheric case is a bit more complicated than what is - written here I think. To come soon...) - -\item[time-discretization] \ - - The time steps are set through the real variables \textbf{deltaTMom} - and \textbf{deltaTtracer} (in s) which represent the time step for - the momentum and tracer equations, respectively. For synchronous - integrations, simply set the two variables to the same value (or you - can prescribe one time step only through the variable - \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set - through the variable \textbf{abEps} (dimensionless). The stagger - baroclinic time stepping can be activated by setting the logical - variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}. - -\end{description} - - -\subsection{Equation of state} - -First, because the model equations are written in terms of -perturbations, a reference thermodynamic state needs to be specified. -This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}. -\textbf{tRef} specifies the reference potential temperature profile -(in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting -from the level k=1. Similarly, \textbf{sRef} specifies the reference -salinity profile (in ppt) for the ocean or the reference specific -humidity profile (in g/kg) for the atmosphere. - -The form of the equation of state is controlled by the character -variables \textbf{buoyancyRelation} and \textbf{eosType}. -\textbf{buoyancyRelation} is set to \texttt{'OCEANIC'} by default and -needs to be set to \texttt{'ATMOSPHERIC'} for atmosphere simulations. -In this case, \textbf{eosType} must be set to \texttt{'IDEALGAS'}. -For the ocean, two forms of the equation of state are available: -linear (set \textbf{eosType} to \texttt{'LINEAR'}) and a polynomial -approximation to the full nonlinear equation ( set \textbf{eosType} to -\texttt{'POLYNOMIAL'}). In the linear case, you need to specify the -thermal and haline expansion coefficients represented by the variables -\textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For -the nonlinear case, you need to generate a file of polynomial -coefficients called \textit{POLY3.COEFFS}. To do this, use the program -\textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is -available in the same directory and you will need to edit the number -and the values of the vertical levels in \textit{knudsen2.f} so that -they match those of your configuration). - -There there are also higher polynomials for the equation of state: -\begin{description} -\item[\texttt{'UNESCO'}:] The UNESCO equation of state formula of - Fofonoff and Millard \cite{fofonoff83}. This equation of state - assumes in-situ temperature, which is not a model variable; {\em its - use is therefore discouraged, and it is only listed for - completeness}. -\item[\texttt{'JMD95Z'}:] A modified UNESCO formula by Jackett and - McDougall \cite{jackett95}, which uses the model variable potential - temperature as input. The \texttt{'Z'} indicates that this equation - of state uses a horizontally and temporally constant pressure - $p_{0}=-g\rho_{0}z$. -\item[\texttt{'JMD95P'}:] A modified UNESCO formula by Jackett and - McDougall \cite{jackett95}, which uses the model variable potential - temperature as input. The \texttt{'P'} indicates that this equation - of state uses the actual hydrostatic pressure of the last time - step. Lagging the pressure in this way requires an additional pickup - file for restarts. -\item[\texttt{'MDJWF'}:] The new, more accurate and less expensive - equation of state by McDougall et~al. \cite{mcdougall03}. It also - requires lagging the pressure and therefore an additional pickup - file for restarts. -\end{description} -For none of these options an reference profile of temperature or -salinity is required. - -\subsection{Momentum equations} - -In this section, we only focus for now on the parameters that you are -likely to change, i.e. the ones relative to forcing and dissipation -for example. The details relevant to the vector-invariant form of the -equations and the various advection schemes are not covered for the -moment. We assume that you use the standard form of the momentum -equations (i.e. the flux-form) with the default advection scheme. -Also, there are a few logical variables that allow you to turn on/off -various terms in the momentum equation. These variables are called -\textbf{momViscosity, momAdvection, momForcing, useCoriolis, - momPressureForcing, momStepping} and \textbf{metricTerms }and are -assumed to be set to \texttt{'.TRUE.'} here. Look at the file -\textit{model/inc/PARAMS.h }for a precise definition of these -variables. - -\begin{description} -\item[initialization] \ - - The velocity components are initialized to 0 unless the simulation - is starting from a pickup file (see section on simulation control - parameters). - -\item[forcing] \ - - This section only applies to the ocean. You need to generate - wind-stress data into two files \textbf{zonalWindFile} and - \textbf{meridWindFile} corresponding to the zonal and meridional - components of the wind stress, respectively (if you want the stress - to be along the direction of only one of the model horizontal axes, - you only need to generate one file). The format of the files is - similar to the bathymetry file. The zonal (meridional) stress data - are assumed to be in Pa and located at U-points (V-points). As for - the bathymetry, the precision with which to read the binary data is - controlled by the variable \textbf{readBinaryPrec}. See the matlab - program \textit{gendata.m} in the \textit{input} directories under - \textit{verification} to see how simple analytical wind forcing data - are generated for the case study experiments. - - There is also the possibility of prescribing time-dependent periodic - forcing. To do this, concatenate the successive time records into a - single file (for each stress component) ordered in a (x,y,t) fashion - and set the following variables: \textbf{periodicExternalForcing }to - \texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s) - of which the forcing varies (typically 1 month), and - \textbf{externForcingCycle} to the repeat time (in s) of the forcing - (typically 1 year -- note: \textbf{ externForcingCycle} must be a - multiple of \textbf{externForcingPeriod}). With these variables set - up, the model will interpolate the forcing linearly at each - iteration. - -\item[dissipation] \ - - The lateral eddy viscosity coefficient is specified through the - variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy - viscosity coefficient is specified through the variable - \textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and - \textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere. The - vertical diffusive fluxes can be computed implicitly by setting the - logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}. - In addition, biharmonic mixing can be added as well through the - variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar - grid, you might also need to set the variable \textbf{cosPower} - which is set to 0 by default and which represents the power of - cosine of latitude to multiply viscosity. Slip or no-slip conditions - at lateral and bottom boundaries are specified through the logical - variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If - set to \texttt{'.FALSE.'}, free-slip boundary conditions are - applied. If no-slip boundary conditions are applied at the bottom, a - bottom drag can be applied as well. Two forms are available: linear - (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and - quadratic (set the variable \textbf{bottomDragQuadratic} in - m$^{-1}$). - - The Fourier and Shapiro filters are described elsewhere. - -\item[C-D scheme] \ - - If you run at a sufficiently coarse resolution, you will need the - C-D scheme for the computation of the Coriolis terms. The - variable\textbf{\ tauCD}, which represents the C-D scheme coupling - timescale (in s) needs to be set. - -\item[calculation of pressure/geopotential] \ - - First, to run a non-hydrostatic ocean simulation, set the logical - variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure - field is then inverted through a 3D elliptic equation. (Note: this - capability is not available for the atmosphere yet.) By default, a - hydrostatic simulation is assumed and a 2D elliptic equation is used - to invert the pressure field. The parameters controlling the - behaviour of the elliptic solvers are the variables - \textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for - the 2D case and \textbf{cg3dMaxIters} and - \textbf{cg3dTargetResidual} for the 3D case. You probably won't need to - alter the default values (are we sure of this?). - - For the calculation of the surface pressure (for the ocean) or - surface geopotential (for the atmosphere) you need to set the - logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface} - (set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'} - depending on how you want to deal with the ocean upper or atmosphere - lower boundary). - -\end{description} - -\subsection{Tracer equations} - -This section covers the tracer equations i.e. the potential -temperature equation and the salinity (for the ocean) or specific -humidity (for the atmosphere) equation. As for the momentum equations, -we only describe for now the parameters that you are likely to change. -The logical variables \textbf{tempDiffusion} \textbf{tempAdvection} -\textbf{tempForcing}, and \textbf{tempStepping} allow you to turn -on/off terms in the temperature equation (same thing for salinity or -specific humidity with variables \textbf{saltDiffusion}, -\textbf{saltAdvection} etc.). These variables are all assumed here to -be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h} -for a precise definition. - -\begin{description} -\item[initialization] \ - - The initial tracer data can be contained in the binary files - \textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files - should contain 3D data ordered in an (x,y,r) fashion with k=1 as the - first vertical level. If no file names are provided, the tracers - are then initialized with the values of \textbf{tRef} and - \textbf{sRef} mentioned above (in the equation of state section). In - this case, the initial tracer data are uniform in x and y for each - depth level. - -\item[forcing] \ - - This part is more relevant for the ocean, the procedure for the - atmosphere not being completely stabilized at the moment. - - A combination of fluxes data and relaxation terms can be used for - driving the tracer equations. For potential temperature, heat flux - data (in W/m$ ^{2}$) can be stored in the 2D binary file - \textbf{surfQfile}. Alternatively or in addition, the forcing can - be specified through a relaxation term. The SST data to which the - model surface temperatures are restored to are supposed to be stored - in the 2D binary file \textbf{thetaClimFile}. The corresponding - relaxation time scale coefficient is set through the variable - \textbf{tauThetaClimRelax} (in s). The same procedure applies for - salinity with the variable names \textbf{EmPmRfile}, - \textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater - flux (in m/s) and surface salinity (in ppt) data files and - relaxation time scale coefficient (in s), respectively. Also for - salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, - natural boundary conditions are applied i.e. when computing the - surface salinity tendency, the freshwater flux is multiplied by the - model surface salinity instead of a constant salinity value. - - As for the other input files, the precision with which to read the - data is controlled by the variable \textbf{readBinaryPrec}. - Time-dependent, periodic forcing can be applied as well following - the same procedure used for the wind forcing data (see above). - -\item[dissipation] \ - - Lateral eddy diffusivities for temperature and salinity/specific - humidity are specified through the variables \textbf{diffKhT} and - \textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are - specified through the variables \textbf{diffKzT} and - \textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT - }and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The - vertical diffusive fluxes can be computed implicitly by setting the - logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}. - In addition, biharmonic diffusivities can be specified as well - through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in - m$^{4}$/s). Note that the cosine power scaling (specified through - \textbf{cosPower}---see the momentum equations section) is applied to - the tracer diffusivities (Laplacian and biharmonic) as well. The - Gent and McWilliams parameterization for oceanic tracers is - described in the package section. Finally, note that tracers can be - also subject to Fourier and Shapiro filtering (see the corresponding - section on these filters). - -\item[ocean convection] \ - - Two options are available to parameterize ocean convection: one is - to use the convective adjustment scheme. In this case, you need to - set the variable \textbf{cadjFreq}, which represents the frequency - (in s) with which the adjustment algorithm is called, to a non-zero - value (if set to a negative value by the user, the model will set it - to the tracer time step). The other option is to parameterize - convection with implicit vertical diffusion. To do this, set the - logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'} - and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s) - you wish the tracer vertical diffusivities to have when mixing - tracers vertically due to static instabilities. Note that - \textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero - value. - -\end{description} - -\subsection{Simulation controls} - -The model ''clock'' is defined by the variable \textbf{deltaTClock} -(in s) which determines the IO frequencies and is used in tagging -output. Typically, you will set it to the tracer time step for -accelerated runs (otherwise it is simply set to the default time step -\textbf{deltaT}). Frequency of checkpointing and dumping of the model -state are referenced to this clock (see below). - -\begin{description} -\item[run duration] \ - - The beginning of a simulation is set by specifying a start time (in - s) through the real variable \textbf{startTime} or by specifying an - initial iteration number through the integer variable - \textbf{nIter0}. If these variables are set to nonzero values, the - model will look for a ''pickup'' file \textit{pickup.0000nIter0} to - restart the integration. The end of a simulation is set through the - real variable \textbf{endTime} (in s). Alternatively, you can - specify instead the number of time steps to execute through the - integer variable \textbf{nTimeSteps}. - -\item[frequency of output] \ - - Real variables defining frequencies (in s) with which output files - are written on disk need to be set up. \textbf{dumpFreq} controls - the frequency with which the instantaneous state of the model is - saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output - frequency of rolling and permanent checkpoint files, respectively. - See section 1.5.1 Output files for the definition of model state and - checkpoint files. In addition, time-averaged fields can be written - out by setting the variable \textbf{taveFreq} (in s). The precision - with which to write the binary data is controlled by the integer - variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or - \texttt{64}). - -\end{description} - - -%%% Local Variables: -%%% mode: latex -%%% TeX-master: t -%%% End: +Similar scripts for netCDF output (\texttt{rdmnc.m}) are available.