| 79 |
|
|
| 80 |
\end{enumerate} |
\end{enumerate} |
| 81 |
|
|
| 82 |
|
\subsection{Method 1 - Checkout from CVS} |
| 83 |
|
\label{sect:cvs_checkout} |
| 84 |
|
|
| 85 |
If CVS is available on your system, we strongly encourage you to use it. CVS |
If CVS is available on your system, we strongly encourage you to use it. CVS |
| 86 |
provides an efficient and elegant way of organizing your code and keeping |
provides an efficient and elegant way of organizing your code and keeping |
| 87 |
track of your changes. If CVS is not available on your machine, you can also |
track of your changes. If CVS is not available on your machine, you can also |
| 96 |
\begin{verbatim} |
\begin{verbatim} |
| 97 |
% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
| 98 |
\end{verbatim} |
\end{verbatim} |
| 99 |
in your .profile or .bashrc file. |
in your \texttt{.profile} or \texttt{.bashrc} file. |
| 100 |
|
|
| 101 |
|
|
| 102 |
To get MITgcm through CVS, first register with the MITgcm CVS server |
To get MITgcm through CVS, first register with the MITgcm CVS server |
| 124 |
\end{verbatim} |
\end{verbatim} |
| 125 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 126 |
|
|
| 127 |
|
As a convenience, the MITgcm CVS server contains aliases which are |
| 128 |
|
named subsets of the codebase. These aliases can be especially |
| 129 |
|
helpful when used over slow internet connections or on machines with |
| 130 |
|
restricted storage space. Table \ref{tab:cvsModules} contains a list |
| 131 |
|
of CVS aliases |
| 132 |
|
\begin{table}[htb] |
| 133 |
|
\centering |
| 134 |
|
\begin{tabular}[htb]{|lp{3.25in}|}\hline |
| 135 |
|
\textbf{Alias Name} & \textbf{Information (directories) Contained} \\\hline |
| 136 |
|
\texttt{MITgcm\_code} & Only the source code -- none of the verification examples. \\ |
| 137 |
|
\texttt{MITgcm\_verif\_basic} |
| 138 |
|
& Source code plus a small set of the verification examples |
| 139 |
|
(\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5}, |
| 140 |
|
\texttt{front\_relax}, and \texttt{plume\_on\_slope}). \\ |
| 141 |
|
\texttt{MITgcm\_verif\_atmos} & Source code plus all of the atmospheric examples. \\ |
| 142 |
|
\texttt{MITgcm\_verif\_ocean} & Source code plus all of the oceanic examples. \\ |
| 143 |
|
\texttt{MITgcm\_verif\_all} & Source code plus all of the |
| 144 |
|
verification examples. \\\hline |
| 145 |
|
\end{tabular} |
| 146 |
|
\caption{MITgcm CVS Modules} |
| 147 |
|
\label{tab:cvsModules} |
| 148 |
|
\end{table} |
| 149 |
|
|
| 150 |
The checkout process creates a directory called \textit{MITgcm}. If |
The checkout process creates a directory called \textit{MITgcm}. If |
| 151 |
the directory \textit{MITgcm} exists this command updates your code |
the directory \textit{MITgcm} exists this command updates your code |
| 159 |
here |
here |
| 160 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 161 |
. |
. |
| 162 |
|
It is important to note that the CVS aliases in Table |
| 163 |
|
\ref{tab:cvsModules} cannot be used in conjunction with the CVS |
| 164 |
|
\texttt{-d DIRNAME} option. However, the \texttt{MITgcm} directories |
| 165 |
|
they create can be changed to a different name following the check-out: |
| 166 |
|
\begin{verbatim} |
| 167 |
|
% cvs co MITgcm_verif_basic |
| 168 |
|
% mv MITgcm MITgcm_verif_basic |
| 169 |
|
\end{verbatim} |
| 170 |
|
|
| 171 |
|
|
| 172 |
\paragraph*{Conventional download method} |
\subsection{Method 2 - Tar file download} |
| 173 |
\label{sect:conventionalDownload} |
\label{sect:conventionalDownload} |
| 174 |
|
|
| 175 |
If you do not have CVS on your system, you can download the model as a |
If you do not have CVS on your system, you can download the model as a |
| 189 |
\begin{rawhtml} </A> \end{rawhtml} |
\begin{rawhtml} </A> \end{rawhtml} |
| 190 |
mailing list. |
mailing list. |
| 191 |
|
|
| 192 |
\paragraph*{Upgrading from an earlier version} |
\subsubsection{Upgrading from an earlier version} |
| 193 |
|
|
| 194 |
If you already have an earlier version of the code you can ``upgrade'' |
If you already have an earlier version of the code you can ``upgrade'' |
| 195 |
your copy instead of downloading the entire repository again. First, |
your copy instead of downloading the entire repository again. First, |
| 324 |
|
|
| 325 |
\end{itemize} |
\end{itemize} |
| 326 |
|
|
| 327 |
\section{Example experiments} |
\section[MITgcm Example Experiments]{Example experiments} |
| 328 |
\label{sect:modelExamples} |
\label{sect:modelExamples} |
| 329 |
|
|
| 330 |
%% a set of twenty-four pre-configured numerical experiments |
%% a set of twenty-four pre-configured numerical experiments |
| 484 |
Once you have chosen the example you want to run, you are ready to |
Once you have chosen the example you want to run, you are ready to |
| 485 |
compile the code. |
compile the code. |
| 486 |
|
|
| 487 |
\section{Building the code} |
\section[Building MITgcm]{Building the code} |
| 488 |
\label{sect:buildingCode} |
\label{sect:buildingCode} |
| 489 |
|
|
| 490 |
To compile the code, we use the {\em make} program. This uses a file |
To compile the code, we use the {\em make} program. This uses a file |
| 666 |
\end{verbatim} |
\end{verbatim} |
| 667 |
|
|
| 668 |
|
|
| 669 |
|
\subsection{Using \texttt{genmake2}} |
|
\subsection{Using \textit{genmake2}} |
|
| 670 |
\label{sect:genmake} |
\label{sect:genmake} |
| 671 |
|
|
| 672 |
To compile the code, first use the program \texttt{genmake2} (located |
To compile the code, first use the program \texttt{genmake2} (located |
| 673 |
in the \textit{tools} directory) to generate a Makefile. |
in the \texttt{tools} directory) to generate a Makefile. |
| 674 |
\texttt{genmake2} is a shell script written to work with all |
\texttt{genmake2} is a shell script written to work with all |
| 675 |
``sh''--compatible shells including bash v1, bash v2, and Bourne. |
``sh''--compatible shells including bash v1, bash v2, and Bourne. |
| 676 |
Internally, \texttt{genmake2} determines the locations of needed |
Internally, \texttt{genmake2} determines the locations of needed |
| 677 |
files, the compiler, compiler options, libraries, and Unix tools. It |
files, the compiler, compiler options, libraries, and Unix tools. It |
| 678 |
relies upon a number of ``optfiles'' located in the {\em |
relies upon a number of ``optfiles'' located in the |
| 679 |
tools/build\_options} directory. |
\texttt{tools/build\_options} directory. |
| 680 |
|
|
| 681 |
The purpose of the optfiles is to provide all the compilation options |
The purpose of the optfiles is to provide all the compilation options |
| 682 |
for particular ``platforms'' (where ``platform'' roughly means the |
for particular ``platforms'' (where ``platform'' roughly means the |
| 771 |
the user's path. When these three items have been identified, |
the user's path. When these three items have been identified, |
| 772 |
genmake2 will try to find an optfile that has a matching name. |
genmake2 will try to find an optfile that has a matching name. |
| 773 |
|
|
| 774 |
|
\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default |
| 775 |
|
set of packages to be used. The normal order of precedence for |
| 776 |
|
packages is as follows: |
| 777 |
|
\begin{enumerate} |
| 778 |
|
\item If available, the command line (\texttt{--pdefault}) settings |
| 779 |
|
over-rule any others. |
| 780 |
|
|
| 781 |
|
\item Next, \texttt{genmake2} will look for a file named |
| 782 |
|
``\texttt{packages.conf}'' in the local directory or in any of the |
| 783 |
|
directories specified with the \texttt{--mods} option. |
| 784 |
|
|
| 785 |
|
\item Finally, if neither of the above are available, |
| 786 |
|
\texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file. |
| 787 |
|
\end{enumerate} |
| 788 |
|
|
| 789 |
\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file |
\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file |
| 790 |
used for packages. |
used for packages. |
| 791 |
|
|
| 798 |
assumed that the two packages are compatible and will function |
assumed that the two packages are compatible and will function |
| 799 |
either with or without each other. |
either with or without each other. |
| 800 |
|
|
|
\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default |
|
|
set of packages to be used. |
|
|
|
|
|
If not set, the default package list will be read from {\em |
|
|
pkg/pkg\_default} |
|
|
|
|
| 801 |
\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or |
\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or |
| 802 |
automatic differentiation options file to be used. The file is |
automatic differentiation options file to be used. The file is |
| 803 |
analogous to the ``optfile'' defined above but it specifies |
analogous to the ``optfile'' defined above but it specifies |
| 827 |
``-standarddirs'' option) |
``-standarddirs'' option) |
| 828 |
\end{itemize} |
\end{itemize} |
| 829 |
|
|
| 830 |
|
\item[\texttt{--mpi}] This option enables certain MPI features (using |
| 831 |
|
CPP \texttt{\#define}s) within the code and is necessary for MPI |
| 832 |
|
builds (see Section \ref{sect:mpi-build}). |
| 833 |
|
|
| 834 |
\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of |
\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of |
| 835 |
soft-links and other bugs common with the \texttt{make} versions |
soft-links and other bugs common with the \texttt{make} versions |
| 836 |
provided by commercial Unix vendors, GNU \texttt{make} (sometimes |
provided by commercial Unix vendors, GNU \texttt{make} (sometimes |
| 837 |
called \texttt{gmake}) should be preferred. This option provides a |
called \texttt{gmake}) should be preferred. This option provides a |
| 838 |
means for specifying the make executable to be used. |
means for specifying the make executable to be used. |
| 839 |
|
|
| 840 |
|
\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX) |
| 841 |
|
machines, the ``bash'' shell is unavailable. To run on these |
| 842 |
|
systems, \texttt{genmake2} can be invoked using an ``sh'' (that is, |
| 843 |
|
a Bourne, POSIX, or compatible) shell. The syntax in these |
| 844 |
|
circumstances is: |
| 845 |
|
\begin{center} |
| 846 |
|
\texttt{\% /bin/sh genmake2 -bash=/bin/sh [...options...]} |
| 847 |
|
\end{center} |
| 848 |
|
where \texttt{/bin/sh} can be replaced with the full path and name |
| 849 |
|
of the desired shell. |
| 850 |
|
|
| 851 |
\end{description} |
\end{description} |
| 852 |
|
|
| 853 |
|
|
| 854 |
|
\subsection{Building with MPI} |
| 855 |
|
\label{sect:mpi-build} |
| 856 |
|
|
| 857 |
|
Building MITgcm to use MPI libraries can be complicated due to the |
| 858 |
|
variety of different MPI implementations available, their dependencies |
| 859 |
|
or interactions with different compilers, and their often ad-hoc |
| 860 |
|
locations within file systems. For these reasons, its generally a |
| 861 |
|
good idea to start by finding and reading the documentation for your |
| 862 |
|
machine(s) and, if necessary, seeking help from your local systems |
| 863 |
|
administrator. |
| 864 |
|
|
| 865 |
\section{Running the model} |
The steps for building MITgcm with MPI support are: |
| 866 |
|
\begin{enumerate} |
| 867 |
|
|
| 868 |
|
\item Determine the locations of your MPI-enabled compiler and/or MPI |
| 869 |
|
libraries and put them into an options file as described in Section |
| 870 |
|
\ref{sect:genmake}. One can start with one of the examples in: |
| 871 |
|
\begin{rawhtml} <A |
| 872 |
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/"> |
| 873 |
|
\end{rawhtml} |
| 874 |
|
\begin{center} |
| 875 |
|
\texttt{MITgcm/tools/build\_options/} |
| 876 |
|
\end{center} |
| 877 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 878 |
|
such as \texttt{linux\_ia32\_g77+mpi\_cg01} or |
| 879 |
|
\texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at |
| 880 |
|
hand. You may need help from your user guide or local systems |
| 881 |
|
administrator to determine the exact location of the MPI libraries. |
| 882 |
|
If libraries are not installed, MPI implementations and related |
| 883 |
|
tools are available including: |
| 884 |
|
\begin{itemize} |
| 885 |
|
\item \begin{rawhtml} <A |
| 886 |
|
href="http://www-unix.mcs.anl.gov/mpi/mpich/"> |
| 887 |
|
\end{rawhtml} |
| 888 |
|
MPICH |
| 889 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 890 |
|
|
| 891 |
|
\item \begin{rawhtml} <A |
| 892 |
|
href="http://www.lam-mpi.org/"> |
| 893 |
|
\end{rawhtml} |
| 894 |
|
LAM/MPI |
| 895 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 896 |
|
|
| 897 |
|
\item \begin{rawhtml} <A |
| 898 |
|
href="http://www.osc.edu/~pw/mpiexec/"> |
| 899 |
|
\end{rawhtml} |
| 900 |
|
MPIexec |
| 901 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 902 |
|
\end{itemize} |
| 903 |
|
|
| 904 |
|
\item Build the code with the \texttt{genmake2} \texttt{-mpi} option |
| 905 |
|
(see Section \ref{sect:genmake}) using commands such as: |
| 906 |
|
{\footnotesize \begin{verbatim} |
| 907 |
|
% ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE |
| 908 |
|
% make depend |
| 909 |
|
% make |
| 910 |
|
\end{verbatim} } |
| 911 |
|
|
| 912 |
|
\item Run the code with the appropriate MPI ``run'' or ``exec'' |
| 913 |
|
program provided with your particular implementation of MPI. |
| 914 |
|
Typical MPI packages such as MPICH will use something like: |
| 915 |
|
\begin{verbatim} |
| 916 |
|
% mpirun -np 4 -machinefile mf ./mitgcmuv |
| 917 |
|
\end{verbatim} |
| 918 |
|
Sightly more complicated scripts may be needed for many machines |
| 919 |
|
since execution of the code may be controlled by both the MPI |
| 920 |
|
library and a job scheduling and queueing system such as PBS, |
| 921 |
|
LoadLeveller, Condor, or any of a number of similar tools. A few |
| 922 |
|
example scripts (those used for our \begin{rawhtml} <A |
| 923 |
|
href="http://mitgcm.org/testing.html"> \end{rawhtml}regular |
| 924 |
|
verification runs\begin{rawhtml} </A> \end{rawhtml}) are available |
| 925 |
|
at: |
| 926 |
|
\begin{rawhtml} <A |
| 927 |
|
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/"> |
| 928 |
|
\end{rawhtml} |
| 929 |
|
{\footnotesize \tt |
| 930 |
|
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ } |
| 931 |
|
\begin{rawhtml} </A> \end{rawhtml} |
| 932 |
|
|
| 933 |
|
\end{enumerate} |
| 934 |
|
|
| 935 |
|
An example of the above process on the MITgcm cluster (``cg01'') using |
| 936 |
|
the GNU g77 compiler and the mpich MPI library is: |
| 937 |
|
|
| 938 |
|
{\footnotesize \begin{verbatim} |
| 939 |
|
% cd MITgcm/verification/exp5 |
| 940 |
|
% mkdir build |
| 941 |
|
% cd build |
| 942 |
|
% ../../../tools/genmake2 -mpi -mods=../code \ |
| 943 |
|
-of=../../../tools/build_options/linux_ia32_g77+mpi_cg01 |
| 944 |
|
% make depend |
| 945 |
|
% make |
| 946 |
|
% cd ../input |
| 947 |
|
% /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \ |
| 948 |
|
-machinefile mf --gm-kill 5 -v -np 2 ../build/mitgcmuv |
| 949 |
|
\end{verbatim} } |
| 950 |
|
|
| 951 |
|
|
| 952 |
|
|
| 953 |
|
\section[Running MITgcm]{Running the model in prognostic mode} |
| 954 |
\label{sect:runModel} |
\label{sect:runModel} |
| 955 |
|
|
| 956 |
If compilation finished succesfuully (section \ref{sect:buildModel}) |
If compilation finished succesfuully (section \ref{sect:buildingCode}) |
| 957 |
then an executable called {\em mitgcmuv} will now exist in the local |
then an executable called \texttt{mitgcmuv} will now exist in the |
| 958 |
directory. |
local directory. |
| 959 |
|
|
| 960 |
To run the model as a single process (ie. not in parallel) simply |
To run the model as a single process (ie. not in parallel) simply |
| 961 |
type: |
type: |
| 1059 |
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end |
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end |
| 1060 |
\end{verbatim} |
\end{verbatim} |
| 1061 |
|
|
|
\section{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: |
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