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1.1 |
\section[Customizing MITgcm]{Doing it yourself: customizing the code} |
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1.4 |
\label{sect:customize} |
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edhill |
1.3 |
\begin{rawhtml} |
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<!-- CMIREDIR:customizing_mitgcm: --> |
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\end{rawhtml} |
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cnh |
1.1 |
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When you are ready to run the model in the configuration you want, the |
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easiest thing is to use and adapt the setup of the case studies |
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experiment (described previously) that is the closest to your |
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configuration. Then, the amount of setup will be minimized. In this |
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section, we focus on the setup relative to the ``numerical model'' |
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part of the code (the setup relative to the ``execution environment'' |
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part is covered in the parallel implementation section) and on the |
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variables and parameters that you are likely to change. |
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cnh |
1.2 |
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\subsection{Building/compiling the code elsewhere} |
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In the example above (section \ref{sect:buildingCode}) we built the |
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executable in the {\em input} directory of the experiment for |
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convenience. You can also configure and compile the code in other |
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locations, for example on a scratch disk with out having to copy the |
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entire source tree. The only requirement to do so is you have {\tt |
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genmake2} in your path or you know the absolute path to {\tt |
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genmake2}. |
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The following sections outline some possible methods of organizing |
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your source and data. |
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\subsubsection{Building from the {\em ../code directory}} |
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This is just as simple as building in the {\em input/} directory: |
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\begin{verbatim} |
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% cd verification/exp2/code |
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% ../../../tools/genmake2 |
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% make depend |
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% make |
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\end{verbatim} |
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However, to run the model the executable ({\em mitgcmuv}) and input |
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files must be in the same place. If you only have one calculation to make: |
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\begin{verbatim} |
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% cd ../input |
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% cp ../code/mitgcmuv ./ |
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% ./mitgcmuv > output.txt |
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\end{verbatim} |
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or if you will be making multiple runs with the same executable: |
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\begin{verbatim} |
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% cd ../ |
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% cp -r input run1 |
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% cp code/mitgcmuv run1 |
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% cd run1 |
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% ./mitgcmuv > output.txt |
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\end{verbatim} |
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\subsubsection{Building from a new directory} |
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Since the {\em input} directory contains input files it is often more |
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useful to keep {\em input} pristine and build in a new directory |
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within {\em verification/exp2/}: |
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\begin{verbatim} |
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% cd verification/exp2 |
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% mkdir build |
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% cd build |
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% ../../../tools/genmake2 -mods=../code |
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% make depend |
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% make |
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\end{verbatim} |
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This builds the code exactly as before but this time you need to copy |
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either the executable or the input files or both in order to run the |
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model. For example, |
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\begin{verbatim} |
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% cp ../input/* ./ |
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% ./mitgcmuv > output.txt |
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\end{verbatim} |
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or if you tend to make multiple runs with the same executable then |
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running in a new directory each time might be more appropriate: |
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\begin{verbatim} |
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% cd ../ |
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% mkdir run1 |
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% cp build/mitgcmuv run1/ |
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% cp input/* run1/ |
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% cd run1 |
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% ./mitgcmuv > output.txt |
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\end{verbatim} |
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\subsubsection{Building on a scratch disk} |
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Model object files and output data can use up large amounts of disk |
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space so it is often the case that you will be operating on a large |
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scratch disk. Assuming the model source is in {\em ~/MITgcm} then the |
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following commands will build the model in {\em /scratch/exp2-run1}: |
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\begin{verbatim} |
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% cd /scratch/exp2-run1 |
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% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ |
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-mods=~/MITgcm/verification/exp2/code |
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% make depend |
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% make |
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\end{verbatim} |
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To run the model here, you'll need the input files: |
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\begin{verbatim} |
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% cp ~/MITgcm/verification/exp2/input/* ./ |
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% ./mitgcmuv > output.txt |
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\end{verbatim} |
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As before, you could build in one directory and make multiple runs of |
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the one experiment: |
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\begin{verbatim} |
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% cd /scratch/exp2 |
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% mkdir build |
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% cd build |
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% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ |
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-mods=~/MITgcm/verification/exp2/code |
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% make depend |
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% make |
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% cd ../ |
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% cp -r ~/MITgcm/verification/exp2/input run2 |
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% cd run2 |
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% ./mitgcmuv > output.txt |
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\end{verbatim} |
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\subsection{Using \texttt{genmake2}} |
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\label{sect:genmake} |
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To compile the code, first use the program \texttt{genmake2} (located |
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in the \texttt{tools} directory) to generate a Makefile. |
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\texttt{genmake2} is a shell script written to work with all |
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``sh''--compatible shells including bash v1, bash v2, and Bourne. |
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Internally, \texttt{genmake2} determines the locations of needed |
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files, the compiler, compiler options, libraries, and Unix tools. It |
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relies upon a number of ``optfiles'' located in the |
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\texttt{tools/build\_options} directory. |
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The purpose of the optfiles is to provide all the compilation options |
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for particular ``platforms'' (where ``platform'' roughly means the |
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combination of the hardware and the compiler) and code configurations. |
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Given the combinations of possible compilers and library dependencies |
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({\it eg.} MPI and NetCDF) there may be numerous optfiles available |
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for a single machine. The naming scheme for the majority of the |
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optfiles shipped with the code is |
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\begin{center} |
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{\bf OS\_HARDWARE\_COMPILER } |
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\end{center} |
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where |
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\begin{description} |
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\item[OS] is the name of the operating system (generally the |
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lower-case output of the {\tt 'uname'} command) |
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\item[HARDWARE] is a string that describes the CPU type and |
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corresponds to output from the {\tt 'uname -m'} command: |
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\begin{description} |
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\item[ia32] is for ``x86'' machines such as i386, i486, i586, i686, |
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and athlon |
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\item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2) |
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\item[amd64] is AMD x86\_64 systems |
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\item[ppc] is for Mac PowerPC systems |
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\end{description} |
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\item[COMPILER] is the compiler name (generally, the name of the |
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FORTRAN executable) |
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\end{description} |
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In many cases, the default optfiles are sufficient and will result in |
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usable Makefiles. However, for some machines or code configurations, |
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new ``optfiles'' must be written. To create a new optfile, it is |
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generally best to start with one of the defaults and modify it to suit |
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your needs. Like \texttt{genmake2}, the optfiles are all written |
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using a simple ``sh''--compatible syntax. While nearly all variables |
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used within \texttt{genmake2} may be specified in the optfiles, the |
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critical ones that should be defined are: |
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\begin{description} |
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\item[FC] the FORTRAN compiler (executable) to use |
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\item[DEFINES] the command-line DEFINE options passed to the compiler |
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\item[CPP] the C pre-processor to use |
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\item[NOOPTFLAGS] options flags for special files that should not be |
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optimized |
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\end{description} |
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For example, the optfile for a typical Red Hat Linux machine (``ia32'' |
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architecture) using the GCC (g77) compiler is |
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\begin{verbatim} |
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FC=g77 |
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DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4' |
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CPP='cpp -traditional -P' |
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NOOPTFLAGS='-O0' |
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# For IEEE, use the "-ffloat-store" option |
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if test "x$IEEE" = x ; then |
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FFLAGS='-Wimplicit -Wunused -Wuninitialized' |
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FOPTIM='-O3 -malign-double -funroll-loops' |
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else |
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FFLAGS='-Wimplicit -Wunused -ffloat-store' |
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FOPTIM='-O0 -malign-double' |
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fi |
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\end{verbatim} |
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If you write an optfile for an unrepresented machine or compiler, you |
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are strongly encouraged to submit the optfile to the MITgcm project |
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for inclusion. Please send the file to the |
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\begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml} |
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\begin{center} |
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MITgcm-support@mitgcm.org |
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\end{center} |
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\begin{rawhtml} </A> \end{rawhtml} |
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mailing list. |
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In addition to the optfiles, \texttt{genmake2} supports a number of |
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helpful command-line options. A complete list of these options can be |
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obtained from: |
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\begin{verbatim} |
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% genmake2 -h |
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\end{verbatim} |
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The most important command-line options are: |
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\begin{description} |
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\item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that |
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should be used for a particular build. |
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If no "optfile" is specified (either through the command line or the |
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MITGCM\_OPTFILE environment variable), genmake2 will try to make a |
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reasonable guess from the list provided in {\em |
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tools/build\_options}. The method used for making this guess is |
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to first determine the combination of operating system and hardware |
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(eg. "linux\_ia32") and then find a working FORTRAN compiler within |
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the user's path. When these three items have been identified, |
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genmake2 will try to find an optfile that has a matching name. |
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\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default |
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set of packages to be used. The normal order of precedence for |
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packages is as follows: |
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\begin{enumerate} |
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\item If available, the command line (\texttt{--pdefault}) settings |
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over-rule any others. |
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\item Next, \texttt{genmake2} will look for a file named |
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``\texttt{packages.conf}'' in the local directory or in any of the |
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directories specified with the \texttt{--mods} option. |
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\item Finally, if neither of the above are available, |
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\texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file. |
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\end{enumerate} |
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\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file |
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used for packages. |
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If not specified, the default dependency file {\em pkg/pkg\_depend} |
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is used. The syntax for this file is parsed on a line-by-line basis |
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where each line containes either a comment ("\#") or a simple |
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"PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol |
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specifies a "must be used with" or a "must not be used with" |
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relationship, respectively. If no rule is specified, then it is |
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assumed that the two packages are compatible and will function |
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either with or without each other. |
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\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or |
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automatic differentiation options file to be used. The file is |
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analogous to the ``optfile'' defined above but it specifies |
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information for the AD build process. |
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The default file is located in {\em |
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tools/adjoint\_options/adjoint\_default} and it defines the "TAF" |
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and "TAMC" compilers. An alternate version is also available at |
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{\em tools/adjoint\_options/adjoint\_staf} that selects the newer |
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"STAF" compiler. As with any compilers, it is helpful to have their |
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directories listed in your {\tt \$PATH} environment variable. |
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\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of |
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directories containing ``modifications''. These directories contain |
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files with names that may (or may not) exist in the main MITgcm |
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source tree but will be overridden by any identically-named sources |
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within the ``MODS'' directories. |
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The order of precedence for this "name-hiding" is as follows: |
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\begin{itemize} |
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\item ``MODS'' directories (in the order given) |
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\item Packages either explicitly specified or provided by default |
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(in the order given) |
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\item Packages included due to package dependencies (in the order |
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that that package dependencies are parsed) |
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\item The "standard dirs" (which may have been specified by the |
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``-standarddirs'' option) |
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\end{itemize} |
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\item[\texttt{--mpi}] This option enables certain MPI features (using |
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CPP \texttt{\#define}s) within the code and is necessary for MPI |
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builds (see Section \ref{sect:mpi-build}). |
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\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of |
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soft-links and other bugs common with the \texttt{make} versions |
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provided by commercial Unix vendors, GNU \texttt{make} (sometimes |
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called \texttt{gmake}) should be preferred. This option provides a |
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means for specifying the make executable to be used. |
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\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX) |
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machines, the ``bash'' shell is unavailable. To run on these |
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systems, \texttt{genmake2} can be invoked using an ``sh'' (that is, |
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a Bourne, POSIX, or compatible) shell. The syntax in these |
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circumstances is: |
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\begin{center} |
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\texttt{\% /bin/sh genmake2 -bash=/bin/sh [...options...]} |
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\end{center} |
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where \texttt{/bin/sh} can be replaced with the full path and name |
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of the desired shell. |
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|
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\end{description} |
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\subsection{Building with MPI} |
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\label{sect:mpi-build} |
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Building MITgcm to use MPI libraries can be complicated due to the |
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variety of different MPI implementations available, their dependencies |
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or interactions with different compilers, and their often ad-hoc |
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locations within file systems. For these reasons, its generally a |
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good idea to start by finding and reading the documentation for your |
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machine(s) and, if necessary, seeking help from your local systems |
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administrator. |
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The steps for building MITgcm with MPI support are: |
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\begin{enumerate} |
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|
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\item Determine the locations of your MPI-enabled compiler and/or MPI |
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libraries and put them into an options file as described in Section |
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\ref{sect:genmake}. One can start with one of the examples in: |
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\begin{rawhtml} <A |
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href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/"> |
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\end{rawhtml} |
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\begin{center} |
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\texttt{MITgcm/tools/build\_options/} |
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\end{center} |
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\begin{rawhtml} </A> \end{rawhtml} |
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such as \texttt{linux\_ia32\_g77+mpi\_cg01} or |
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\texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at |
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hand. You may need help from your user guide or local systems |
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administrator to determine the exact location of the MPI libraries. |
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If libraries are not installed, MPI implementations and related |
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tools are available including: |
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\begin{itemize} |
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\item \begin{rawhtml} <A |
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href="http://www-unix.mcs.anl.gov/mpi/mpich/"> |
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\end{rawhtml} |
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MPICH |
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\begin{rawhtml} </A> \end{rawhtml} |
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|
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\item \begin{rawhtml} <A |
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href="http://www.lam-mpi.org/"> |
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\end{rawhtml} |
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LAM/MPI |
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\begin{rawhtml} </A> \end{rawhtml} |
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\item \begin{rawhtml} <A |
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href="http://www.osc.edu/~pw/mpiexec/"> |
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\end{rawhtml} |
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MPIexec |
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\begin{rawhtml} </A> \end{rawhtml} |
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\end{itemize} |
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|
|
\item Build the code with the \texttt{genmake2} \texttt{-mpi} option |
358 |
|
|
(see Section \ref{sect:genmake}) using commands such as: |
359 |
|
|
{\footnotesize \begin{verbatim} |
360 |
|
|
% ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE |
361 |
|
|
% make depend |
362 |
|
|
% make |
363 |
|
|
\end{verbatim} } |
364 |
|
|
|
365 |
|
|
\item Run the code with the appropriate MPI ``run'' or ``exec'' |
366 |
|
|
program provided with your particular implementation of MPI. |
367 |
|
|
Typical MPI packages such as MPICH will use something like: |
368 |
|
|
\begin{verbatim} |
369 |
|
|
% mpirun -np 4 -machinefile mf ./mitgcmuv |
370 |
|
|
\end{verbatim} |
371 |
|
|
Sightly more complicated scripts may be needed for many machines |
372 |
|
|
since execution of the code may be controlled by both the MPI |
373 |
|
|
library and a job scheduling and queueing system such as PBS, |
374 |
|
|
LoadLeveller, Condor, or any of a number of similar tools. A few |
375 |
|
|
example scripts (those used for our \begin{rawhtml} <A |
376 |
|
|
href="http://mitgcm.org/testing.html"> \end{rawhtml}regular |
377 |
|
|
verification runs\begin{rawhtml} </A> \end{rawhtml}) are available |
378 |
|
|
at: |
379 |
|
|
\begin{rawhtml} <A |
380 |
|
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/"> |
381 |
|
|
\end{rawhtml} |
382 |
|
|
{\footnotesize \tt |
383 |
|
|
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ } |
384 |
|
|
\begin{rawhtml} </A> \end{rawhtml} |
385 |
|
|
|
386 |
|
|
\end{enumerate} |
387 |
|
|
|
388 |
|
|
An example of the above process on the MITgcm cluster (``cg01'') using |
389 |
|
|
the GNU g77 compiler and the mpich MPI library is: |
390 |
|
|
|
391 |
|
|
{\footnotesize \begin{verbatim} |
392 |
|
|
% cd MITgcm/verification/exp5 |
393 |
|
|
% mkdir build |
394 |
|
|
% cd build |
395 |
|
|
% ../../../tools/genmake2 -mpi -mods=../code \ |
396 |
|
|
-of=../../../tools/build_options/linux_ia32_g77+mpi_cg01 |
397 |
|
|
% make depend |
398 |
|
|
% make |
399 |
|
|
% cd ../input |
400 |
|
|
% /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \ |
401 |
|
|
-machinefile mf --gm-kill 5 -v -np 2 ../build/mitgcmuv |
402 |
|
|
\end{verbatim} } |
403 |
|
|
|
404 |
cnh |
1.1 |
\subsection{Configuration and setup} |
405 |
|
|
|
406 |
|
|
The CPP keys relative to the ``numerical model'' part of the code are |
407 |
|
|
all defined and set in the file \textit{CPP\_OPTIONS.h }in the |
408 |
|
|
directory \textit{ model/inc }or in one of the \textit{code |
409 |
|
|
}directories of the case study experiments under |
410 |
|
|
\textit{verification.} The model parameters are defined and declared |
411 |
|
|
in the file \textit{model/inc/PARAMS.h }and their default values are |
412 |
|
|
set in the routine \textit{model/src/set\_defaults.F. }The default |
413 |
|
|
values can be modified in the namelist file \textit{data }which needs |
414 |
|
|
to be located in the directory where you will run the model. The |
415 |
|
|
parameters are initialized in the routine |
416 |
|
|
\textit{model/src/ini\_parms.F}. Look at this routine to see in what |
417 |
|
|
part of the namelist the parameters are located. |
418 |
|
|
|
419 |
|
|
In what follows the parameters are grouped into categories related to |
420 |
|
|
the computational domain, the equations solved in the model, and the |
421 |
|
|
simulation controls. |
422 |
|
|
|
423 |
|
|
\subsection{Computational domain, geometry and time-discretization} |
424 |
|
|
|
425 |
|
|
\begin{description} |
426 |
|
|
\item[dimensions] \ |
427 |
|
|
|
428 |
|
|
The number of points in the x, y, and r directions are represented |
429 |
|
|
by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr} |
430 |
|
|
respectively which are declared and set in the file |
431 |
|
|
\textit{model/inc/SIZE.h}. (Again, this assumes a mono-processor |
432 |
|
|
calculation. For multiprocessor calculations see the section on |
433 |
|
|
parallel implementation.) |
434 |
|
|
|
435 |
|
|
\item[grid] \ |
436 |
|
|
|
437 |
|
|
Three different grids are available: cartesian, spherical polar, and |
438 |
|
|
curvilinear (which includes the cubed sphere). The grid is set |
439 |
|
|
through the logical variables \textbf{usingCartesianGrid}, |
440 |
|
|
\textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}. |
441 |
|
|
In the case of spherical and curvilinear grids, the southern |
442 |
|
|
boundary is defined through the variable \textbf{phiMin} which |
443 |
|
|
corresponds to the latitude of the southern most cell face (in |
444 |
|
|
degrees). The resolution along the x and y directions is controlled |
445 |
|
|
by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the |
446 |
|
|
case of a cartesian grid, in degrees otherwise). The vertical grid |
447 |
|
|
spacing is set through the 1D array \textbf{delz} for the ocean (in |
448 |
|
|
meters) or \textbf{delp} for the atmosphere (in Pa). The variable |
449 |
|
|
\textbf{Ro\_SeaLevel} represents the standard position of Sea-Level |
450 |
|
|
in ``R'' coordinate. This is typically set to 0m for the ocean |
451 |
|
|
(default value) and 10$^{5}$Pa for the atmosphere. For the |
452 |
|
|
atmosphere, also set the logical variable \textbf{groundAtK1} to |
453 |
|
|
\texttt{'.TRUE.'} which puts the first level (k=1) at the lower |
454 |
|
|
boundary (ground). |
455 |
|
|
|
456 |
|
|
For the cartesian grid case, the Coriolis parameter $f$ is set |
457 |
|
|
through the variables \textbf{f0} and \textbf{beta} which correspond |
458 |
|
|
to the reference Coriolis parameter (in s$^{-1}$) and |
459 |
|
|
$\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively. |
460 |
|
|
If \textbf{beta } is set to a nonzero value, \textbf{f0} is the |
461 |
|
|
value of $f$ at the southern edge of the domain. |
462 |
|
|
|
463 |
|
|
\item[topography - full and partial cells] \ |
464 |
|
|
|
465 |
|
|
The domain bathymetry is read from a file that contains a 2D (x,y) |
466 |
|
|
map of depths (in m) for the ocean or pressures (in Pa) for the |
467 |
|
|
atmosphere. The file name is represented by the variable |
468 |
|
|
\textbf{bathyFile}. The file is assumed to contain binary numbers |
469 |
|
|
giving the depth (pressure) of the model at each grid cell, ordered |
470 |
|
|
with the x coordinate varying fastest. The points are ordered from |
471 |
|
|
low coordinate to high coordinate for both axes. The model code |
472 |
|
|
applies without modification to enclosed, periodic, and double |
473 |
|
|
periodic domains. Periodicity is assumed by default and is |
474 |
|
|
suppressed by setting the depths to 0m for the cells at the limits |
475 |
|
|
of the computational domain (note: not sure this is the case for the |
476 |
|
|
atmosphere). The precision with which to read the binary data is |
477 |
|
|
controlled by the integer variable \textbf{readBinaryPrec} which can |
478 |
|
|
take the value \texttt{32} (single precision) or \texttt{64} (double |
479 |
|
|
precision). See the matlab program \textit{gendata.m} in the |
480 |
|
|
\textit{input} directories under \textit{verification} to see how |
481 |
|
|
the bathymetry files are generated for the case study experiments. |
482 |
|
|
|
483 |
|
|
To use the partial cell capability, the variable \textbf{hFacMin} |
484 |
|
|
needs to be set to a value between 0 and 1 (it is set to 1 by |
485 |
|
|
default) corresponding to the minimum fractional size of the cell. |
486 |
|
|
For example if the bottom cell is 500m thick and \textbf{hFacMin} is |
487 |
|
|
set to 0.1, the actual thickness of the cell (i.e. used in the code) |
488 |
|
|
can cover a range of discrete values 50m apart from 50m to 500m |
489 |
|
|
depending on the value of the bottom depth (in \textbf{bathyFile}) |
490 |
|
|
at this point. |
491 |
|
|
|
492 |
|
|
Note that the bottom depths (or pressures) need not coincide with |
493 |
|
|
the models levels as deduced from \textbf{delz} or \textbf{delp}. |
494 |
|
|
The model will interpolate the numbers in \textbf{bathyFile} so that |
495 |
|
|
they match the levels obtained from \textbf{delz} or \textbf{delp} |
496 |
|
|
and \textbf{hFacMin}. |
497 |
|
|
|
498 |
|
|
(Note: the atmospheric case is a bit more complicated than what is |
499 |
|
|
written here I think. To come soon...) |
500 |
|
|
|
501 |
|
|
\item[time-discretization] \ |
502 |
|
|
|
503 |
|
|
The time steps are set through the real variables \textbf{deltaTMom} |
504 |
|
|
and \textbf{deltaTtracer} (in s) which represent the time step for |
505 |
|
|
the momentum and tracer equations, respectively. For synchronous |
506 |
|
|
integrations, simply set the two variables to the same value (or you |
507 |
|
|
can prescribe one time step only through the variable |
508 |
|
|
\textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set |
509 |
|
|
through the variable \textbf{abEps} (dimensionless). The stagger |
510 |
|
|
baroclinic time stepping can be activated by setting the logical |
511 |
|
|
variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}. |
512 |
|
|
|
513 |
|
|
\end{description} |
514 |
|
|
|
515 |
|
|
|
516 |
|
|
\subsection{Equation of state} |
517 |
|
|
|
518 |
|
|
First, because the model equations are written in terms of |
519 |
|
|
perturbations, a reference thermodynamic state needs to be specified. |
520 |
|
|
This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}. |
521 |
|
|
\textbf{tRef} specifies the reference potential temperature profile |
522 |
|
|
(in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting |
523 |
|
|
from the level k=1. Similarly, \textbf{sRef} specifies the reference |
524 |
|
|
salinity profile (in ppt) for the ocean or the reference specific |
525 |
|
|
humidity profile (in g/kg) for the atmosphere. |
526 |
|
|
|
527 |
|
|
The form of the equation of state is controlled by the character |
528 |
|
|
variables \textbf{buoyancyRelation} and \textbf{eosType}. |
529 |
|
|
\textbf{buoyancyRelation} is set to \texttt{'OCEANIC'} by default and |
530 |
|
|
needs to be set to \texttt{'ATMOSPHERIC'} for atmosphere simulations. |
531 |
|
|
In this case, \textbf{eosType} must be set to \texttt{'IDEALGAS'}. |
532 |
|
|
For the ocean, two forms of the equation of state are available: |
533 |
|
|
linear (set \textbf{eosType} to \texttt{'LINEAR'}) and a polynomial |
534 |
|
|
approximation to the full nonlinear equation ( set \textbf{eosType} to |
535 |
|
|
\texttt{'POLYNOMIAL'}). In the linear case, you need to specify the |
536 |
|
|
thermal and haline expansion coefficients represented by the variables |
537 |
|
|
\textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For |
538 |
|
|
the nonlinear case, you need to generate a file of polynomial |
539 |
|
|
coefficients called \textit{POLY3.COEFFS}. To do this, use the program |
540 |
|
|
\textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is |
541 |
|
|
available in the same directory and you will need to edit the number |
542 |
|
|
and the values of the vertical levels in \textit{knudsen2.f} so that |
543 |
|
|
they match those of your configuration). |
544 |
|
|
|
545 |
|
|
There there are also higher polynomials for the equation of state: |
546 |
|
|
\begin{description} |
547 |
|
|
\item[\texttt{'UNESCO'}:] The UNESCO equation of state formula of |
548 |
|
|
Fofonoff and Millard \cite{fofonoff83}. This equation of state |
549 |
|
|
assumes in-situ temperature, which is not a model variable; {\em its |
550 |
|
|
use is therefore discouraged, and it is only listed for |
551 |
|
|
completeness}. |
552 |
|
|
\item[\texttt{'JMD95Z'}:] A modified UNESCO formula by Jackett and |
553 |
|
|
McDougall \cite{jackett95}, which uses the model variable potential |
554 |
|
|
temperature as input. The \texttt{'Z'} indicates that this equation |
555 |
|
|
of state uses a horizontally and temporally constant pressure |
556 |
|
|
$p_{0}=-g\rho_{0}z$. |
557 |
|
|
\item[\texttt{'JMD95P'}:] A modified UNESCO formula by Jackett and |
558 |
|
|
McDougall \cite{jackett95}, which uses the model variable potential |
559 |
|
|
temperature as input. The \texttt{'P'} indicates that this equation |
560 |
|
|
of state uses the actual hydrostatic pressure of the last time |
561 |
|
|
step. Lagging the pressure in this way requires an additional pickup |
562 |
|
|
file for restarts. |
563 |
|
|
\item[\texttt{'MDJWF'}:] The new, more accurate and less expensive |
564 |
|
|
equation of state by McDougall et~al. \cite{mcdougall03}. It also |
565 |
|
|
requires lagging the pressure and therefore an additional pickup |
566 |
|
|
file for restarts. |
567 |
|
|
\end{description} |
568 |
|
|
For none of these options an reference profile of temperature or |
569 |
|
|
salinity is required. |
570 |
|
|
|
571 |
|
|
\subsection{Momentum equations} |
572 |
|
|
|
573 |
|
|
In this section, we only focus for now on the parameters that you are |
574 |
|
|
likely to change, i.e. the ones relative to forcing and dissipation |
575 |
|
|
for example. The details relevant to the vector-invariant form of the |
576 |
|
|
equations and the various advection schemes are not covered for the |
577 |
|
|
moment. We assume that you use the standard form of the momentum |
578 |
|
|
equations (i.e. the flux-form) with the default advection scheme. |
579 |
|
|
Also, there are a few logical variables that allow you to turn on/off |
580 |
|
|
various terms in the momentum equation. These variables are called |
581 |
|
|
\textbf{momViscosity, momAdvection, momForcing, useCoriolis, |
582 |
|
|
momPressureForcing, momStepping} and \textbf{metricTerms }and are |
583 |
|
|
assumed to be set to \texttt{'.TRUE.'} here. Look at the file |
584 |
|
|
\textit{model/inc/PARAMS.h }for a precise definition of these |
585 |
|
|
variables. |
586 |
|
|
|
587 |
|
|
\begin{description} |
588 |
|
|
\item[initialization] \ |
589 |
|
|
|
590 |
|
|
The velocity components are initialized to 0 unless the simulation |
591 |
|
|
is starting from a pickup file (see section on simulation control |
592 |
|
|
parameters). |
593 |
|
|
|
594 |
|
|
\item[forcing] \ |
595 |
|
|
|
596 |
|
|
This section only applies to the ocean. You need to generate |
597 |
|
|
wind-stress data into two files \textbf{zonalWindFile} and |
598 |
|
|
\textbf{meridWindFile} corresponding to the zonal and meridional |
599 |
|
|
components of the wind stress, respectively (if you want the stress |
600 |
|
|
to be along the direction of only one of the model horizontal axes, |
601 |
|
|
you only need to generate one file). The format of the files is |
602 |
|
|
similar to the bathymetry file. The zonal (meridional) stress data |
603 |
|
|
are assumed to be in Pa and located at U-points (V-points). As for |
604 |
|
|
the bathymetry, the precision with which to read the binary data is |
605 |
|
|
controlled by the variable \textbf{readBinaryPrec}. See the matlab |
606 |
|
|
program \textit{gendata.m} in the \textit{input} directories under |
607 |
|
|
\textit{verification} to see how simple analytical wind forcing data |
608 |
|
|
are generated for the case study experiments. |
609 |
|
|
|
610 |
|
|
There is also the possibility of prescribing time-dependent periodic |
611 |
|
|
forcing. To do this, concatenate the successive time records into a |
612 |
|
|
single file (for each stress component) ordered in a (x,y,t) fashion |
613 |
|
|
and set the following variables: \textbf{periodicExternalForcing }to |
614 |
|
|
\texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s) |
615 |
|
|
of which the forcing varies (typically 1 month), and |
616 |
|
|
\textbf{externForcingCycle} to the repeat time (in s) of the forcing |
617 |
|
|
(typically 1 year -- note: \textbf{ externForcingCycle} must be a |
618 |
|
|
multiple of \textbf{externForcingPeriod}). With these variables set |
619 |
|
|
up, the model will interpolate the forcing linearly at each |
620 |
|
|
iteration. |
621 |
|
|
|
622 |
|
|
\item[dissipation] \ |
623 |
|
|
|
624 |
|
|
The lateral eddy viscosity coefficient is specified through the |
625 |
|
|
variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy |
626 |
|
|
viscosity coefficient is specified through the variable |
627 |
|
|
\textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and |
628 |
|
|
\textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere. The |
629 |
|
|
vertical diffusive fluxes can be computed implicitly by setting the |
630 |
|
|
logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}. |
631 |
|
|
In addition, biharmonic mixing can be added as well through the |
632 |
|
|
variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar |
633 |
|
|
grid, you might also need to set the variable \textbf{cosPower} |
634 |
|
|
which is set to 0 by default and which represents the power of |
635 |
|
|
cosine of latitude to multiply viscosity. Slip or no-slip conditions |
636 |
|
|
at lateral and bottom boundaries are specified through the logical |
637 |
|
|
variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If |
638 |
|
|
set to \texttt{'.FALSE.'}, free-slip boundary conditions are |
639 |
|
|
applied. If no-slip boundary conditions are applied at the bottom, a |
640 |
|
|
bottom drag can be applied as well. Two forms are available: linear |
641 |
jmc |
1.5 |
(set the variable \textbf{bottomDragLinear} in m/s) and |
642 |
|
|
quadratic (set the variable \textbf{bottomDragQuadratic}, dimensionless). |
643 |
cnh |
1.1 |
|
644 |
|
|
The Fourier and Shapiro filters are described elsewhere. |
645 |
|
|
|
646 |
|
|
\item[C-D scheme] \ |
647 |
|
|
|
648 |
|
|
If you run at a sufficiently coarse resolution, you will need the |
649 |
|
|
C-D scheme for the computation of the Coriolis terms. The |
650 |
|
|
variable\textbf{\ tauCD}, which represents the C-D scheme coupling |
651 |
|
|
timescale (in s) needs to be set. |
652 |
|
|
|
653 |
|
|
\item[calculation of pressure/geopotential] \ |
654 |
|
|
|
655 |
|
|
First, to run a non-hydrostatic ocean simulation, set the logical |
656 |
|
|
variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure |
657 |
|
|
field is then inverted through a 3D elliptic equation. (Note: this |
658 |
|
|
capability is not available for the atmosphere yet.) By default, a |
659 |
|
|
hydrostatic simulation is assumed and a 2D elliptic equation is used |
660 |
|
|
to invert the pressure field. The parameters controlling the |
661 |
|
|
behaviour of the elliptic solvers are the variables |
662 |
|
|
\textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for |
663 |
|
|
the 2D case and \textbf{cg3dMaxIters} and |
664 |
|
|
\textbf{cg3dTargetResidual} for the 3D case. You probably won't need to |
665 |
|
|
alter the default values (are we sure of this?). |
666 |
|
|
|
667 |
|
|
For the calculation of the surface pressure (for the ocean) or |
668 |
|
|
surface geopotential (for the atmosphere) you need to set the |
669 |
|
|
logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface} |
670 |
|
|
(set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'} |
671 |
|
|
depending on how you want to deal with the ocean upper or atmosphere |
672 |
|
|
lower boundary). |
673 |
|
|
|
674 |
|
|
\end{description} |
675 |
|
|
|
676 |
|
|
\subsection{Tracer equations} |
677 |
|
|
|
678 |
|
|
This section covers the tracer equations i.e. the potential |
679 |
|
|
temperature equation and the salinity (for the ocean) or specific |
680 |
|
|
humidity (for the atmosphere) equation. As for the momentum equations, |
681 |
|
|
we only describe for now the parameters that you are likely to change. |
682 |
|
|
The logical variables \textbf{tempDiffusion} \textbf{tempAdvection} |
683 |
|
|
\textbf{tempForcing}, and \textbf{tempStepping} allow you to turn |
684 |
|
|
on/off terms in the temperature equation (same thing for salinity or |
685 |
|
|
specific humidity with variables \textbf{saltDiffusion}, |
686 |
|
|
\textbf{saltAdvection} etc.). These variables are all assumed here to |
687 |
|
|
be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h} |
688 |
|
|
for a precise definition. |
689 |
|
|
|
690 |
|
|
\begin{description} |
691 |
|
|
\item[initialization] \ |
692 |
|
|
|
693 |
|
|
The initial tracer data can be contained in the binary files |
694 |
|
|
\textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files |
695 |
|
|
should contain 3D data ordered in an (x,y,r) fashion with k=1 as the |
696 |
|
|
first vertical level. If no file names are provided, the tracers |
697 |
|
|
are then initialized with the values of \textbf{tRef} and |
698 |
|
|
\textbf{sRef} mentioned above (in the equation of state section). In |
699 |
|
|
this case, the initial tracer data are uniform in x and y for each |
700 |
|
|
depth level. |
701 |
|
|
|
702 |
|
|
\item[forcing] \ |
703 |
|
|
|
704 |
|
|
This part is more relevant for the ocean, the procedure for the |
705 |
|
|
atmosphere not being completely stabilized at the moment. |
706 |
|
|
|
707 |
|
|
A combination of fluxes data and relaxation terms can be used for |
708 |
|
|
driving the tracer equations. For potential temperature, heat flux |
709 |
|
|
data (in W/m$ ^{2}$) can be stored in the 2D binary file |
710 |
|
|
\textbf{surfQfile}. Alternatively or in addition, the forcing can |
711 |
|
|
be specified through a relaxation term. The SST data to which the |
712 |
|
|
model surface temperatures are restored to are supposed to be stored |
713 |
|
|
in the 2D binary file \textbf{thetaClimFile}. The corresponding |
714 |
|
|
relaxation time scale coefficient is set through the variable |
715 |
|
|
\textbf{tauThetaClimRelax} (in s). The same procedure applies for |
716 |
|
|
salinity with the variable names \textbf{EmPmRfile}, |
717 |
|
|
\textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater |
718 |
|
|
flux (in m/s) and surface salinity (in ppt) data files and |
719 |
|
|
relaxation time scale coefficient (in s), respectively. Also for |
720 |
|
|
salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, |
721 |
|
|
natural boundary conditions are applied i.e. when computing the |
722 |
|
|
surface salinity tendency, the freshwater flux is multiplied by the |
723 |
|
|
model surface salinity instead of a constant salinity value. |
724 |
|
|
|
725 |
|
|
As for the other input files, the precision with which to read the |
726 |
|
|
data is controlled by the variable \textbf{readBinaryPrec}. |
727 |
|
|
Time-dependent, periodic forcing can be applied as well following |
728 |
|
|
the same procedure used for the wind forcing data (see above). |
729 |
|
|
|
730 |
|
|
\item[dissipation] \ |
731 |
|
|
|
732 |
|
|
Lateral eddy diffusivities for temperature and salinity/specific |
733 |
|
|
humidity are specified through the variables \textbf{diffKhT} and |
734 |
|
|
\textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are |
735 |
|
|
specified through the variables \textbf{diffKzT} and |
736 |
|
|
\textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT |
737 |
|
|
}and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The |
738 |
|
|
vertical diffusive fluxes can be computed implicitly by setting the |
739 |
|
|
logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}. |
740 |
|
|
In addition, biharmonic diffusivities can be specified as well |
741 |
|
|
through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in |
742 |
|
|
m$^{4}$/s). Note that the cosine power scaling (specified through |
743 |
|
|
\textbf{cosPower}---see the momentum equations section) is applied to |
744 |
|
|
the tracer diffusivities (Laplacian and biharmonic) as well. The |
745 |
|
|
Gent and McWilliams parameterization for oceanic tracers is |
746 |
|
|
described in the package section. Finally, note that tracers can be |
747 |
|
|
also subject to Fourier and Shapiro filtering (see the corresponding |
748 |
|
|
section on these filters). |
749 |
|
|
|
750 |
|
|
\item[ocean convection] \ |
751 |
|
|
|
752 |
|
|
Two options are available to parameterize ocean convection: one is |
753 |
|
|
to use the convective adjustment scheme. In this case, you need to |
754 |
|
|
set the variable \textbf{cadjFreq}, which represents the frequency |
755 |
|
|
(in s) with which the adjustment algorithm is called, to a non-zero |
756 |
|
|
value (if set to a negative value by the user, the model will set it |
757 |
|
|
to the tracer time step). The other option is to parameterize |
758 |
|
|
convection with implicit vertical diffusion. To do this, set the |
759 |
|
|
logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'} |
760 |
|
|
and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s) |
761 |
|
|
you wish the tracer vertical diffusivities to have when mixing |
762 |
|
|
tracers vertically due to static instabilities. Note that |
763 |
|
|
\textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero |
764 |
|
|
value. |
765 |
|
|
|
766 |
|
|
\end{description} |
767 |
|
|
|
768 |
|
|
\subsection{Simulation controls} |
769 |
|
|
|
770 |
|
|
The model ''clock'' is defined by the variable \textbf{deltaTClock} |
771 |
|
|
(in s) which determines the IO frequencies and is used in tagging |
772 |
|
|
output. Typically, you will set it to the tracer time step for |
773 |
|
|
accelerated runs (otherwise it is simply set to the default time step |
774 |
|
|
\textbf{deltaT}). Frequency of checkpointing and dumping of the model |
775 |
|
|
state are referenced to this clock (see below). |
776 |
|
|
|
777 |
|
|
\begin{description} |
778 |
|
|
\item[run duration] \ |
779 |
|
|
|
780 |
|
|
The beginning of a simulation is set by specifying a start time (in |
781 |
|
|
s) through the real variable \textbf{startTime} or by specifying an |
782 |
|
|
initial iteration number through the integer variable |
783 |
|
|
\textbf{nIter0}. If these variables are set to nonzero values, the |
784 |
|
|
model will look for a ''pickup'' file \textit{pickup.0000nIter0} to |
785 |
|
|
restart the integration. The end of a simulation is set through the |
786 |
|
|
real variable \textbf{endTime} (in s). Alternatively, you can |
787 |
|
|
specify instead the number of time steps to execute through the |
788 |
|
|
integer variable \textbf{nTimeSteps}. |
789 |
|
|
|
790 |
|
|
\item[frequency of output] \ |
791 |
|
|
|
792 |
|
|
Real variables defining frequencies (in s) with which output files |
793 |
|
|
are written on disk need to be set up. \textbf{dumpFreq} controls |
794 |
|
|
the frequency with which the instantaneous state of the model is |
795 |
|
|
saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output |
796 |
|
|
frequency of rolling and permanent checkpoint files, respectively. |
797 |
|
|
See section 1.5.1 Output files for the definition of model state and |
798 |
|
|
checkpoint files. In addition, time-averaged fields can be written |
799 |
|
|
out by setting the variable \textbf{taveFreq} (in s). The precision |
800 |
|
|
with which to write the binary data is controlled by the integer |
801 |
|
|
variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or |
802 |
|
|
\texttt{64}). |
803 |
|
|
|
804 |
|
|
\end{description} |
805 |
|
|
|
806 |
|
|
|
807 |
|
|
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808 |
|
|
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|
|
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810 |
|
|
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