--- manual/s_getstarted/text/customization.tex 2004/10/14 14:54:24 1.2 +++ manual/s_getstarted/text/customization.tex 2010/08/30 23:09:20 1.11 @@ -1,4 +1,8 @@ -\section[Customizing MITgcm]{Doing it yourself: customizing the code} +\section[Customizing MITgcm]{Doing it yourself: customizing the model configuration} +\label{sec:customize} +\begin{rawhtml} + +\end{rawhtml} 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 @@ -9,396 +13,6 @@ part is covered in the parallel implementation section) and on the variables and parameters that you are likely to change. - -\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} } - -\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 @@ -410,13 +24,18 @@ 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. +part of the namelist the parameters are located. Here is a complete list +of the model parameters related to the main model (namelist parameters +for the packages are located in the package descriptions), their meaning, +and their default values: + +\input{s_getstarted/text/main-parms.tex} 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} +\subsection{Parameters: Computational domain, geometry and time-discretization} \begin{description} \item[dimensions] \ @@ -435,7 +54,7 @@ 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 + boundary is defined through the variable \textbf{ygOrigin} 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 @@ -509,7 +128,7 @@ \end{description} -\subsection{Equation of state} +\subsection{Parameters: Equation of state} First, because the model equations are written in terms of perturbations, a reference thermodynamic state needs to be specified. @@ -564,7 +183,7 @@ For none of these options an reference profile of temperature or salinity is required. -\subsection{Momentum equations} +\subsection{Parameters: 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 @@ -583,9 +202,19 @@ \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). + The initial horizontal velocity components can be specified from + binary files \textbf{uVelInitFile} and \textbf{vVelInitFile}. + These files should contain 3D data ordered in an (x,y,r) fashion with + k=1 as the first vertical level (surface level). + If no file names are provided, the velocity is initialised to zero. + The initial vertical velocity is always derived from the horizontal velocity + using the continuity equation, even in the case of non-hydrostatic simulation + (see, e.g.: {\it tutorial\_deep\_convection/input/data}). + + In the case of a restart (from the end of a previous simulation), + the velocity field is read from a pickup file + (see section on simulation control parameters) + and the initial velocity files are ignored. \item[forcing] \ @@ -634,9 +263,8 @@ 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}$). + (set the variable \textbf{bottomDragLinear} in m/s) and + quadratic (set the variable \textbf{bottomDragQuadratic}, dimensionless). The Fourier and Shapiro filters are described elsewhere. @@ -670,7 +298,7 @@ \end{description} -\subsection{Tracer equations} +\subsection{Parameters: Tracer equations} This section covers the tracer equations i.e. the potential temperature equation and the salinity (for the ocean) or specific @@ -762,7 +390,7 @@ \end{description} -\subsection{Simulation controls} +\subsection{Parameters: Simulation controls} The model ''clock'' is defined by the variable \textbf{deltaTClock} (in s) which determines the IO frequencies and is used in tagging