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%\section{Getting started} |
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\begin{center} |
In this section, we describe how to use the model. In the first |
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{\Large \textbf{Using the model}} |
section, we provide enough information to help you get started with |
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the model. We believe the best way to familiarize yourself with the |
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model is to run the case study examples provided with the base |
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version. Information on how to obtain, compile, and run the code is |
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found there as well as a brief description of the model structure |
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directory and the case study examples. The latter and the code |
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structure are described more fully in chapters |
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\ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in |
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this section, we provide information on how to customize the code when |
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you are ready to try implementing the configuration you have in mind. |
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\vspace*{4mm} |
\section{Where to find information} |
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\label{sect:whereToFindInfo} |
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\vspace*{3mm} {\large July 2001} |
A web site is maintained for release 2 (``Pelican'') of MITgcm: |
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\end{center} |
\begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml} |
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\begin{verbatim} |
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http://mitgcm.org/pelican |
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\end{verbatim} |
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\begin{rawhtml} </A> \end{rawhtml} |
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Here you will find an on-line version of this document, a |
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``browsable'' copy of the code and a searchable database of the model |
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and site, as well as links for downloading the model and |
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documentation, to data-sources, and other related sites. |
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There is also a web-archived support mailing list for the model that |
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you can email at \texttt{MITgcm-support@mitgcm.org} or browse at: |
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\begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml} |
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\begin{verbatim} |
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http://mitgcm.org/mailman/listinfo/mitgcm-support/ |
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http://mitgcm.org/pipermail/mitgcm-support/ |
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\end{verbatim} |
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\begin{rawhtml} </A> \end{rawhtml} |
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Essentially all of the MITgcm web pages can be searched using a |
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popular web crawler such as Google or through our own search facility: |
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\begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml} |
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\begin{verbatim} |
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http://mitgcm.org/htdig/ |
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\end{verbatim} |
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\begin{rawhtml} </A> \end{rawhtml} |
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%%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org |
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In this part, we describe how to use the model. In the first section, we |
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provide enough information to help you get started with the model. We |
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believe the best way to familiarize yourself with the model is to run the |
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case study examples provided with the base version. Information on how to |
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obtain, compile, and run the code is found there as well as a brief |
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description of the model structure directory and the case study examples. |
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The latter and the code structure are described more fully in sections 2 and |
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3, respectively. In section 4, we provide information on how to customize |
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the code when you are ready to try implementing the configuration you have |
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in mind. |
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\section{Getting started} |
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\subsection{Obtaining the code} |
\section{Obtaining the code} |
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\label{sect:obtainingCode} |
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The reference web site for the model is: |
MITgcm can be downloaded from our system by following |
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\begin{verbatim} |
the instructions below. As a courtesy we ask that you send e-mail to us at |
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http://mitgcm.org |
\begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml} |
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\end{verbatim} |
MITgcm-support@mitgcm.org |
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\begin{rawhtml} </A> \end{rawhtml} |
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to enable us to keep track of who's using the model and in what application. |
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You can download the model two ways: |
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\begin{enumerate} |
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\item Using CVS software. CVS is a freely available source code management |
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tool. To use CVS you need to have the software installed. Many systems |
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come with CVS pre-installed, otherwise good places to look for |
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the software for a particular platform are |
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\begin{rawhtml} <A href=http://www.cvshome.org/ target="idontexist"> \end{rawhtml} |
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cvshome.org |
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\begin{rawhtml} </A> \end{rawhtml} |
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and |
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\begin{rawhtml} <A href=http://www.wincvs.org/ target="idontexist"> \end{rawhtml} |
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wincvs.org |
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\begin{rawhtml} </A> \end{rawhtml} |
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. |
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\item Using a tar file. This method is simple and does not |
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require any special software. However, this method does not |
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provide easy support for maintenance updates. |
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On this site, you can download the model as well as find useful information, |
\end{enumerate} |
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some of which might overlap with what is written here. There is also a |
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support news group for the model located at (send your message to \texttt{% |
\subsubsection{Checkout from CVS} |
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support@mitgcm.org}): |
\label{sect:cvs_checkout} |
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\begin{verbatim} |
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news://mitgcm.org/mitgcm.support |
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\end{verbatim} |
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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 |
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provides an efficient and elegant way of organizing your code and keeping |
provides an efficient and elegant way of organizing your code and keeping |
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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 |
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download a tar file. |
download a tar file. |
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\subsubsection{using CVS} |
Before you can use CVS, the following environment variable(s) should |
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be set within your shell. For a csh or tcsh shell, put the following |
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\begin{verbatim} |
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% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack |
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\end{verbatim} |
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in your .cshrc or .tcshrc file. For bash or sh shells, put: |
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\begin{verbatim} |
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% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' |
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\end{verbatim} |
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in your \texttt{.profile} or \texttt{.bashrc} file. |
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Before you can use CVS, the following environment variable has to be set in |
To get MITgcm through CVS, first register with the MITgcm CVS server |
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your .cshrc or .tcshrc: |
using command: |
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\begin{verbatim} |
\begin{verbatim} |
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% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack |
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% cvs login ( CVS password: cvsanon ) |
% cvs login ( CVS password: cvsanon ) |
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\end{verbatim} |
\end{verbatim} |
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You only need to do a ``cvs login'' once. |
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You only need to do ``cvs login'' once. To obtain the latest source: |
To obtain the latest sources type: |
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\begin{verbatim} |
\begin{verbatim} |
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% cvs co -d directory models/MITgcmUV |
% cvs co MITgcm |
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\end{verbatim} |
\end{verbatim} |
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or to get a specific release type: |
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\begin{verbatim} |
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% cvs co -P -r checkpoint52i_post MITgcm |
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\end{verbatim} |
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The MITgcm web site contains further directions concerning the source |
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code and CVS. It also contains a web interface to our CVS archive so |
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that one may easily view the state of files, revisions, and other |
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development milestones: |
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\begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml} |
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\begin{verbatim} |
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http://mitgcm.org/source_code.html |
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\end{verbatim} |
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\begin{rawhtml} </A> \end{rawhtml} |
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This creates a directory called \textit{directory}. If \textit{directory} |
As a convenience, the MITgcm CVS server contains aliases which are |
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exists this command updates your code based on the repository. Each |
named subsets of the codebase. These aliases can be especially |
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directory in the source tree contains a directory \textit{CVS}. This |
helpful when used over slow internet connections or on machines with |
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information is required by CVS to keep track of your file versions with |
restricted storage space. Table \ref{tab:cvsModules} contains a list |
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respect to the repository. Don't edit the files in \textit{CVS}! To obtain a |
of CVS aliases |
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specific \textit{version} that is not the latest source: |
\begin{table}[htb] |
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\centering |
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\begin{tabular}[htb]{|lp{3.25in}|}\hline |
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\textbf{Alias Name} & \textbf{Information (directories) Contained} \\\hline |
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\texttt{MITgcm\_code} & Only the source code -- none of the verification examples. \\ |
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\texttt{MITgcm\_verif\_basic} |
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& Source code plus a small set of the verification examples |
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(\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5}, |
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\texttt{front\_relax}, and \texttt{plume\_on\_slope}). \\ |
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\texttt{MITgcm\_verif\_atmos} & Source code plus all of the atmospheric examples. \\ |
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\texttt{MITgcm\_verif\_ocean} & Source code plus all of the oceanic examples. \\ |
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\texttt{MITgcm\_verif\_all} & Source code plus all of the |
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verification examples. \\\hline |
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\end{tabular} |
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\caption{MITgcm CVS Modules} |
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\label{tab:cvsModules} |
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\end{table} |
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The checkout process creates a directory called \textit{MITgcm}. If |
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the directory \textit{MITgcm} exists this command updates your code |
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based on the repository. Each directory in the source tree contains a |
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directory \textit{CVS}. This information is required by CVS to keep |
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track of your file versions with respect to the repository. Don't edit |
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the files in \textit{CVS}! You can also use CVS to download code |
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updates. More extensive information on using CVS for maintaining |
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MITgcm code can be found |
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\begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml} |
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here |
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\begin{rawhtml} </A> \end{rawhtml} |
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. |
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It is important to note that the CVS aliases in Table |
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\ref{tab:cvsModules} cannot be used in conjunction with the CVS |
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\texttt{-d DIRNAME} option. However, the \texttt{MITgcm} directories |
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they create can be changed to a different name following the check-out: |
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\begin{verbatim} |
\begin{verbatim} |
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% cvs co -d directory -r version models/MITgcmUV |
% cvs co MITgcm_verif_basic |
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% mv MITgcm MITgcm_verif_basic |
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\end{verbatim} |
\end{verbatim} |
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\subsubsection{other methods} |
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You can download the model as a tar file from the reference web site at: |
\subsubsection{Conventional download method} |
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\label{sect:conventionalDownload} |
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If you do not have CVS on your system, you can download the model as a |
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tar file from the web site at: |
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\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml} |
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\begin{verbatim} |
\begin{verbatim} |
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http://mitgcm.org/download/ |
http://mitgcm.org/download/ |
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\end{verbatim} |
\end{verbatim} |
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\begin{rawhtml} </A> \end{rawhtml} |
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\subsection{Model and directory structure} |
The tar file still contains CVS information which we urge you not to |
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delete; even if you do not use CVS yourself the information can help |
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The ``numerical'' model is contained within a execution environment support |
us if you should need to send us your copy of the code. If a recent |
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wrapper. This wrapper is designed to provide a general framework for |
tar file does not exist, then please contact the developers through |
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grid-point models. MITgcmUV is a specific numerical model that uses the |
the |
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framework. Under this structure the model is split into execution |
\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
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environment support code and conventional numerical model code. The |
MITgcm-support@mitgcm.org |
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execution environment support code is held under the \textit{eesupp} |
\begin{rawhtml} </A> \end{rawhtml} |
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directory. The grid point model code is held under the \textit{model} |
mailing list. |
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directory. Code execution actually starts in the \textit{eesupp} routines |
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and not in the \textit{model} routines. For this reason the top-level |
\subsubsection{Upgrading from an earlier version} |
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\textit{MAIN.F} is in the \textit{eesupp/src} directory. In general, |
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end-users should not need to worry about this level. The top-level routine |
If you already have an earlier version of the code you can ``upgrade'' |
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for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F% |
your copy instead of downloading the entire repository again. First, |
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}. Here is a brief description of the directory structure of the model under |
``cd'' (change directory) to the top of your working copy: |
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the root tree (a detailed description is given in section 3: Code structure). |
\begin{verbatim} |
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% cd MITgcm |
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\end{verbatim} |
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and then issue the cvs update command such as: |
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\begin{verbatim} |
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% cvs -q update -r checkpoint52i_post -d -P |
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\end{verbatim} |
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This will update the ``tag'' to ``checkpoint52i\_post'', add any new |
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directories (-d) and remove any empty directories (-P). The -q option |
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means be quiet which will reduce the number of messages you'll see in |
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the terminal. If you have modified the code prior to upgrading, CVS |
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will try to merge your changes with the upgrades. If there is a |
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conflict between your modifications and the upgrade, it will report |
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that file with a ``C'' in front, e.g.: |
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\begin{verbatim} |
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C model/src/ini_parms.F |
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\end{verbatim} |
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If the list of conflicts scrolled off the screen, you can re-issue the |
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cvs update command and it will report the conflicts. Conflicts are |
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indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and |
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``$>>>>>>>$''. For example, |
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{\small |
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\begin{verbatim} |
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<<<<<<< ini_parms.F |
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& bottomDragLinear,myOwnBottomDragCoefficient, |
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======= |
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& bottomDragLinear,bottomDragQuadratic, |
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>>>>>>> 1.18 |
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\end{verbatim} |
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} |
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means that you added ``myOwnBottomDragCoefficient'' to a namelist at |
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the same time and place that we added ``bottomDragQuadratic''. You |
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need to resolve this conflict and in this case the line should be |
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changed to: |
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{\small |
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\begin{verbatim} |
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& bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient, |
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\end{verbatim} |
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} |
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and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted. |
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Unless you are making modifications which exactly parallel |
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developments we make, these types of conflicts should be rare. |
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\paragraph*{Upgrading to the current pre-release version} |
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We don't make a ``release'' for every little patch and bug fix in |
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order to keep the frequency of upgrades to a minimum. However, if you |
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have run into a problem for which ``we have already fixed in the |
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latest code'' and we haven't made a ``tag'' or ``release'' since that |
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patch then you'll need to get the latest code: |
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\begin{verbatim} |
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% cvs -q update -A -d -P |
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\end{verbatim} |
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Unlike, the ``check-out'' and ``update'' procedures above, there is no |
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``tag'' or release name. The -A tells CVS to upgrade to the |
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very latest version. As a rule, we don't recommend this since you |
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might upgrade while we are in the processes of checking in the code so |
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that you may only have part of a patch. Using this method of updating |
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also means we can't tell what version of the code you are working |
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with. So please be sure you understand what you're doing. |
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\section{Model and directory structure} |
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The ``numerical'' model is contained within a execution environment |
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support wrapper. This wrapper is designed to provide a general |
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framework for grid-point models. MITgcmUV is a specific numerical |
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model that uses the framework. Under this structure the model is split |
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into execution environment support code and conventional numerical |
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model code. The execution environment support code is held under the |
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\textit{eesupp} directory. The grid point model code is held under the |
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\textit{model} directory. Code execution actually starts in the |
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\textit{eesupp} routines and not in the \textit{model} routines. For |
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this reason the top-level \textit{MAIN.F} is in the |
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\textit{eesupp/src} directory. In general, end-users should not need |
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to worry about this level. The top-level routine for the numerical |
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part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is |
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a brief description of the directory structure of the model under the |
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root tree (a detailed description is given in section 3: Code |
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structure). |
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\begin{itemize} |
\begin{itemize} |
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\item \textit{bin}: this directory is initially empty. It is the default |
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directory in which to compile the code. |
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\item \textit{bin}: this directory is initially empty. It is the |
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default directory in which to compile the code. |
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\item \textit{diags}: contains the code relative to time-averaged |
\item \textit{diags}: contains the code relative to time-averaged |
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diagnostics. It is subdivided into two subdirectories \textit{inc} and |
diagnostics. It is subdivided into two subdirectories \textit{inc} |
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\textit{src} that contain include files (*.\textit{h} files) and fortran |
and \textit{src} that contain include files (*.\textit{h} files) and |
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subroutines (*.\textit{F} files), respectively. |
Fortran subroutines (*.\textit{F} files), respectively. |
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\item \textit{doc}: contains brief documentation notes. |
\item \textit{doc}: contains brief documentation notes. |
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\item \textit{eesupp}: contains the execution environment source code. Also |
\item \textit{eesupp}: contains the execution environment source code. |
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subdivided into two subdirectories \textit{inc} and \textit{src}. |
Also subdivided into two subdirectories \textit{inc} and |
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\textit{src}. |
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\item \textit{exe}: this directory is initially empty. It is the default |
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directory in which to execute the code. |
\item \textit{exe}: this directory is initially empty. It is the |
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default directory in which to execute the code. |
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\item \textit{model}: this directory contains the main source code. Also |
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subdivided into two subdirectories \textit{inc} and \textit{src}. |
\item \textit{model}: this directory contains the main source code. |
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Also subdivided into two subdirectories \textit{inc} and |
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\item \textit{pkg}: contains the source code for the packages. Each package |
\textit{src}. |
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corresponds to a subdirectory. For example, \textit{gmredi} contains the |
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code related to the Gent-McWilliams/Redi scheme, \textit{aim} the code |
\item \textit{pkg}: contains the source code for the packages. Each |
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relative to the atmospheric intermediate physics. The packages are described |
package corresponds to a subdirectory. For example, \textit{gmredi} |
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in detail in section 3. |
contains the code related to the Gent-McWilliams/Redi scheme, |
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\textit{aim} the code relative to the atmospheric intermediate |
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\item \textit{tools}: this directory contains various useful tools. For |
physics. The packages are described in detail in section 3. |
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example, \textit{genmake} is a script written in csh (C-shell) that should |
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be used to generate your makefile. The directory \textit{adjoint} contains |
\item \textit{tools}: this directory contains various useful tools. |
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the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that |
For example, \textit{genmake2} is a script written in csh (C-shell) |
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generates the adjoint code. The latter is described in details in part V. |
that should be used to generate your makefile. The directory |
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\textit{adjoint} contains the makefile specific to the Tangent |
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linear and Adjoint Compiler (TAMC) that generates the adjoint code. |
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The latter is described in details in part V. |
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\item \textit{utils}: this directory contains various utilities. The |
\item \textit{utils}: this directory contains various utilities. The |
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subdirectory \textit{knudsen2} contains code and a makefile that compute |
subdirectory \textit{knudsen2} contains code and a makefile that |
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coefficients of the polynomial approximation to the knudsen formula for an |
compute coefficients of the polynomial approximation to the knudsen |
316 |
ocean nonlinear equation of state. The \textit{matlab} subdirectory contains |
formula for an ocean nonlinear equation of state. The |
317 |
matlab scripts for reading model output directly into matlab. \textit{scripts% |
\textit{matlab} subdirectory contains matlab scripts for reading |
318 |
} contains C-shell post-processing scripts for joining processor-based and |
model output directly into matlab. \textit{scripts} contains C-shell |
319 |
tiled-based model output. |
post-processing scripts for joining processor-based and tiled-based |
320 |
|
model output. |
321 |
|
|
322 |
|
\item \textit{verification}: this directory contains the model |
323 |
|
examples. See section \ref{sect:modelExamples}. |
324 |
|
|
|
\item \textit{verification}: this directory contains the model examples. See |
|
|
below. |
|
325 |
\end{itemize} |
\end{itemize} |
326 |
|
|
327 |
\subsection{Model examples} |
\section{Example experiments} |
328 |
|
\label{sect:modelExamples} |
329 |
Now that you have successfully downloaded the model code we recommend that |
|
330 |
you first try to run the examples provided with the base version. You will |
%% a set of twenty-four pre-configured numerical experiments |
331 |
probably want to run the example that is the closest to the configuration |
|
332 |
you will use eventually. The examples are located in subdirectories under |
The MITgcm distribution comes with more than a dozen pre-configured |
333 |
the directory \textit{verification} and are briefly described below (a full |
numerical experiments. Some of these example experiments are tests of |
334 |
description is given in section 2): |
individual parts of the model code, but many are fully fledged |
335 |
|
numerical simulations. A few of the examples are used for tutorial |
336 |
|
documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}. |
337 |
|
The other examples follow the same general structure as the tutorial |
338 |
|
examples. However, they only include brief instructions in a text file |
339 |
|
called {\it README}. The examples are located in subdirectories under |
340 |
|
the directory \textit{verification}. Each example is briefly described |
341 |
|
below. |
342 |
|
|
343 |
\subsubsection{List of model examples} |
\subsection{Full list of model examples} |
344 |
|
|
345 |
\begin{itemize} |
\begin{enumerate} |
346 |
|
|
347 |
\item \textit{exp0} - single layer, ocean double gyre (barotropic with |
\item \textit{exp0} - single layer, ocean double gyre (barotropic with |
348 |
free-surface). |
free-surface). This experiment is described in detail in section |
349 |
|
\ref{sect:eg-baro}. |
|
\item \textit{exp1} - 4 layers, ocean double gyre. |
|
350 |
|
|
351 |
|
\item \textit{exp1} - Four layer, ocean double gyre. This experiment |
352 |
|
is described in detail in section \ref{sect:eg-baroc}. |
353 |
|
|
354 |
\item \textit{exp2} - 4x4 degree global ocean simulation with steady |
\item \textit{exp2} - 4x4 degree global ocean simulation with steady |
355 |
climatological forcing. |
climatological forcing. This experiment is described in detail in |
356 |
|
section \ref{sect:eg-global}. |
357 |
\item \textit{exp4} - flow over a Gaussian bump in open-water or channel |
|
358 |
with open boundaries. |
\item \textit{exp4} - Flow over a Gaussian bump in open-water or |
359 |
|
channel with open boundaries. |
360 |
|
|
361 |
|
\item \textit{exp5} - Inhomogenously forced ocean convection in a |
362 |
|
doubly periodic box. |
363 |
|
|
364 |
\item \textit{exp5} - inhomogenously forced ocean convection in a doubly |
\item \textit{front\_relax} - Relaxation of an ocean thermal front (test for |
|
periodic box. |
|
|
|
|
|
\item \textit{front\_relax} - relaxation of an ocean thermal front (test for |
|
365 |
Gent/McWilliams scheme). 2D (Y-Z). |
Gent/McWilliams scheme). 2D (Y-Z). |
366 |
|
|
367 |
\item \textit{internal wave} - ocean internal wave forced by open boundary |
\item \textit{internal wave} - Ocean internal wave forced by open |
368 |
conditions. |
boundary conditions. |
369 |
|
|
370 |
\item \textit{natl\_box} - eastern subtropical North Atlantic with KPP |
\item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP |
371 |
scheme; 1 month integration |
scheme; 1 month integration |
372 |
|
|
373 |
\item \textit{hs94.1x64x5} - zonal averaged atmosphere using Held and Suarez |
\item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and |
374 |
'94 forcing. |
Suarez '94 forcing. |
375 |
|
|
376 |
\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez |
\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and |
377 |
'94 forcing. |
Suarez '94 forcing. |
378 |
|
|
379 |
\item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and |
\item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and |
380 |
Suarez '94 forcing on the cubed sphere. |
Suarez '94 forcing on the cubed sphere. |
381 |
|
|
382 |
\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics, 5 layers |
\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics. |
383 |
Molteni physics package. Global Zonal Mean configuration, 1x64x5 resolution. |
Global Zonal Mean configuration, 1x64x5 resolution. |
384 |
|
|
385 |
\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric |
\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate |
386 |
physics, 5 layers Molteni physics package. Equatorial Slice configuration. |
Atmospheric physics, equatorial Slice configuration. 2D (X-Z). |
387 |
2D (X-Z). |
|
|
|
|
388 |
\item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric |
\item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric |
389 |
physics, 5 layers Molteni physics package. 3D Equatorial Channel |
physics. 3D Equatorial Channel configuration. |
390 |
configuration (not completely tested). |
|
391 |
|
\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics. |
392 |
\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers |
Global configuration, on latitude longitude grid with 128x64x5 grid |
393 |
Molteni physics package. Global configuration, 128x64x5 resolution. |
points ($2.8^\circ{\rm degree}$ resolution). |
394 |
|
|
395 |
|
\item \textit{adjustment.128x64x1} Barotropic adjustment problem on |
396 |
|
latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm |
397 |
|
degree}$ resolution). |
398 |
|
|
399 |
|
\item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on |
400 |
|
cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm |
401 |
|
degree}$ resolution). |
402 |
|
|
403 |
|
\item \textit{advect\_cs} Two-dimensional passive advection test on |
404 |
|
cube sphere grid. |
405 |
|
|
406 |
|
\item \textit{advect\_xy} Two-dimensional (horizontal plane) passive |
407 |
|
advection test on Cartesian grid. |
408 |
|
|
409 |
|
\item \textit{advect\_yz} Two-dimensional (vertical plane) passive |
410 |
|
advection test on Cartesian grid. |
411 |
|
|
412 |
|
\item \textit{carbon} Simple passive tracer experiment. Includes |
413 |
|
derivative calculation. Described in detail in section |
414 |
|
\ref{sect:eg-carbon-ad}. |
415 |
|
|
416 |
|
\item \textit{flt\_example} Example of using float package. |
417 |
|
|
418 |
|
\item \textit{global\_ocean.90x40x15} Global circulation with GM, flux |
419 |
|
boundary conditions and poles. |
420 |
|
|
421 |
|
\item \textit{global\_ocean\_pressure} Global circulation in pressure |
422 |
|
coordinate (non-Boussinesq ocean model). Described in detail in |
423 |
|
section \ref{sect:eg-globalpressure}. |
424 |
|
|
425 |
|
\item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube |
426 |
|
sphere grid. |
427 |
|
|
428 |
\item \textit{adjustment.128x64x1} |
\end{enumerate} |
429 |
|
|
430 |
\item \textit{adjustment.cs-32x32x1} |
\subsection{Directory structure of model examples} |
|
\end{itemize} |
|
|
|
|
|
\subsubsection{Directory structure of model examples} |
|
431 |
|
|
432 |
Each example directory has the following subdirectories: |
Each example directory has the following subdirectories: |
433 |
|
|
434 |
\begin{itemize} |
\begin{itemize} |
435 |
\item \textit{code}: contains the code particular to the example. At a |
\item \textit{code}: contains the code particular to the example. At a |
436 |
minimum, this directory includes the following files: |
minimum, this directory includes the following files: |
|
|
|
|
\begin{itemize} |
|
|
\item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to the |
|
|
``execution environment'' part of the code. The default version is located |
|
|
in \textit{eesupp/inc}. |
|
|
|
|
|
\item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the |
|
|
``numerical model'' part of the code. The default version is located in |
|
|
\textit{model/inc}. |
|
|
|
|
|
\item \textit{code/SIZE.h}: declares size of underlying computational grid. |
|
|
The default version is located in \textit{model/inc}. |
|
|
\end{itemize} |
|
|
|
|
|
In addition, other include files and subroutines might be present in \textit{% |
|
|
code} depending on the particular experiment. See section 2 for more details. |
|
|
|
|
|
\item \textit{input}: contains the input data files required to run the |
|
|
example. At a mimimum, the \textit{input} directory contains the following |
|
|
files: |
|
|
|
|
|
\begin{itemize} |
|
|
\item \textit{input/data}: this file, written as a namelist, specifies the |
|
|
main parameters for the experiment. |
|
437 |
|
|
438 |
\item \textit{input/data.pkg}: contains parameters relative to the packages |
\begin{itemize} |
439 |
used in the experiment. |
\item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to |
440 |
|
the ``execution environment'' part of the code. The default |
441 |
|
version is located in \textit{eesupp/inc}. |
442 |
|
|
443 |
|
\item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to |
444 |
|
the ``numerical model'' part of the code. The default version is |
445 |
|
located in \textit{model/inc}. |
446 |
|
|
447 |
|
\item \textit{code/SIZE.h}: declares size of underlying |
448 |
|
computational grid. The default version is located in |
449 |
|
\textit{model/inc}. |
450 |
|
\end{itemize} |
451 |
|
|
452 |
|
In addition, other include files and subroutines might be present in |
453 |
|
\textit{code} depending on the particular experiment. See Section 2 |
454 |
|
for more details. |
455 |
|
|
456 |
|
\item \textit{input}: contains the input data files required to run |
457 |
|
the example. At a minimum, the \textit{input} directory contains the |
458 |
|
following files: |
459 |
|
|
460 |
|
\begin{itemize} |
461 |
|
\item \textit{input/data}: this file, written as a namelist, |
462 |
|
specifies the main parameters for the experiment. |
463 |
|
|
464 |
|
\item \textit{input/data.pkg}: contains parameters relative to the |
465 |
|
packages used in the experiment. |
466 |
|
|
467 |
|
\item \textit{input/eedata}: this file contains ``execution |
468 |
|
environment'' data. At present, this consists of a specification |
469 |
|
of the number of threads to use in $X$ and $Y$ under multithreaded |
470 |
|
execution. |
471 |
|
\end{itemize} |
472 |
|
|
473 |
|
In addition, you will also find in this directory the forcing and |
474 |
|
topography files as well as the files describing the initial state |
475 |
|
of the experiment. This varies from experiment to experiment. See |
476 |
|
section 2 for more details. |
477 |
|
|
478 |
|
\item \textit{results}: this directory contains the output file |
479 |
|
\textit{output.txt} produced by the simulation example. This file is |
480 |
|
useful for comparison with your own output when you run the |
481 |
|
experiment. |
482 |
|
\end{itemize} |
483 |
|
|
484 |
|
Once you have chosen the example you want to run, you are ready to |
485 |
|
compile the code. |
486 |
|
|
487 |
|
\section{Building the code} |
488 |
|
\label{sect:buildingCode} |
489 |
|
|
490 |
|
To compile the code, we use the {\em make} program. This uses a file |
491 |
|
({\em Makefile}) that allows us to pre-process source files, specify |
492 |
|
compiler and optimization options and also figures out any file |
493 |
|
dependencies. We supply a script ({\em genmake2}), described in |
494 |
|
section \ref{sect:genmake}, that automatically creates the {\em |
495 |
|
Makefile} for you. You then need to build the dependencies and |
496 |
|
compile the code. |
497 |
|
|
498 |
|
As an example, let's assume that you want to build and run experiment |
499 |
|
\textit{verification/exp2}. The are multiple ways and places to |
500 |
|
actually do this but here let's build the code in |
501 |
|
\textit{verification/exp2/input}: |
502 |
|
\begin{verbatim} |
503 |
|
% cd verification/exp2/input |
504 |
|
\end{verbatim} |
505 |
|
First, build the {\em Makefile}: |
506 |
|
\begin{verbatim} |
507 |
|
% ../../../tools/genmake2 -mods=../code |
508 |
|
\end{verbatim} |
509 |
|
The command line option tells {\em genmake} to override model source |
510 |
|
code with any files in the directory {\em ./code/}. |
511 |
|
|
512 |
\item \textit{input/eedata}: this file contains ``execution environment'' |
On many systems, the {\em genmake2} program will be able to |
513 |
data. At present, this consists of a specification of the number of threads |
automatically recognize the hardware, find compilers and other tools |
514 |
to use in $X$ and $Y$ under multithreaded execution. |
within the user's path (``echo \$PATH''), and then choose an |
515 |
\end{itemize} |
appropriate set of options from the files contained in the {\em |
516 |
|
tools/build\_options} directory. Under some circumstances, a user |
517 |
|
may have to create a new ``optfile'' in order to specify the exact |
518 |
|
combination of compiler, compiler flags, libraries, and other options |
519 |
|
necessary to build a particular configuration of MITgcm. In such |
520 |
|
cases, it is generally helpful to read the existing ``optfiles'' and |
521 |
|
mimic their syntax. |
522 |
|
|
523 |
|
Through the MITgcm-support list, the MITgcm developers are willing to |
524 |
|
provide help writing or modifing ``optfiles''. And we encourage users |
525 |
|
to post new ``optfiles'' (particularly ones for new machines or |
526 |
|
architectures) to the |
527 |
|
\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
528 |
|
MITgcm-support@mitgcm.org |
529 |
|
\begin{rawhtml} </A> \end{rawhtml} |
530 |
|
list. |
531 |
|
|
532 |
In addition, you will also find in this directory the forcing and topography |
To specify an optfile to {\em genmake2}, the syntax is: |
533 |
files as well as the files describing the initial state of the experiment. |
\begin{verbatim} |
534 |
This varies from experiment to experiment. See section 2 for more details. |
% ../../../tools/genmake2 -mods=../code -of /path/to/optfile |
535 |
|
\end{verbatim} |
|
\item \textit{results}: this directory contains the output file \textit{% |
|
|
output.txt} produced by the simulation example. This file is useful for |
|
|
comparison with your own output when you run the experiment. |
|
|
\end{itemize} |
|
536 |
|
|
537 |
Once you have chosen the example you want to run, you are ready to compile |
Once a {\em Makefile} has been generated, we create the dependencies: |
538 |
the code. |
\begin{verbatim} |
539 |
|
% make depend |
540 |
|
\end{verbatim} |
541 |
|
This modifies the {\em Makefile} by attaching a [long] list of files |
542 |
|
upon which other files depend. The purpose of this is to reduce |
543 |
|
re-compilation if and when you start to modify the code. The {\tt make |
544 |
|
depend} command also creates links from the model source to this |
545 |
|
directory. |
546 |
|
|
547 |
\subsection{Compiling the code} |
Next compile the code: |
548 |
|
\begin{verbatim} |
549 |
|
% make |
550 |
|
\end{verbatim} |
551 |
|
The {\tt make} command creates an executable called \textit{mitgcmuv}. |
552 |
|
Additional make ``targets'' are defined within the makefile to aid in |
553 |
|
the production of adjoint and other versions of MITgcm. |
554 |
|
|
555 |
\subsubsection{The script \textit{genmake}} |
Now you are ready to run the model. General instructions for doing so are |
556 |
|
given in section \ref{sect:runModel}. Here, we can run the model with: |
557 |
|
\begin{verbatim} |
558 |
|
./mitgcmuv > output.txt |
559 |
|
\end{verbatim} |
560 |
|
where we are re-directing the stream of text output to the file {\em |
561 |
|
output.txt}. |
562 |
|
|
|
To compile the code, use the script \textit{genmake} located in the \textit{% |
|
|
tools} directory. \textit{genmake} is a script that generates the makefile. |
|
|
It has been written so that the code can be compiled on a wide diversity of |
|
|
machines and systems. However, if it doesn't work the first time on your |
|
|
platform, you might need to edit certain lines of \textit{genmake} in the |
|
|
section containing the setups for the different machines. The file is |
|
|
structured like this: |
|
|
\begin{verbatim} |
|
|
. |
|
|
. |
|
|
. |
|
|
general instructions (machine independent) |
|
|
. |
|
|
. |
|
|
. |
|
|
- setup machine 1 |
|
|
- setup machine 2 |
|
|
- setup machine 3 |
|
|
- setup machine 4 |
|
|
etc |
|
|
. |
|
|
. |
|
|
. |
|
|
\end{verbatim} |
|
|
|
|
|
For example, the setup corresponding to a DEC alpha machine is reproduced |
|
|
here: |
|
|
\begin{verbatim} |
|
|
case OSF1+mpi: |
|
|
echo "Configuring for DEC Alpha" |
|
|
set CPP = ( '/usr/bin/cpp -P' ) |
|
|
set DEFINES = ( ${DEFINES} '-DTARGET_DEC -DWORDLENGTH=1' ) |
|
|
set KPP = ( 'kapf' ) |
|
|
set KPPFILES = ( 'main.F' ) |
|
|
set KFLAGS1 = ( '-scan=132 -noconc -cmp=' ) |
|
|
set FC = ( 'f77' ) |
|
|
set FFLAGS = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' ) |
|
|
set FOPTIM = ( '-O5 -fast -tune host -inline all' ) |
|
|
set NOOPTFLAGS = ( '-O0' ) |
|
|
set LIBS = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' ) |
|
|
set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F') |
|
|
set RMFILES = ( '*.p.out' ) |
|
|
breaksw |
|
|
\end{verbatim} |
|
|
|
|
|
Typically, these are the lines that you might need to edit to make \textit{% |
|
|
genmake} work on your platform if it doesn't work the first time. \textit{% |
|
|
genmake} understands several options that are described here: |
|
563 |
|
|
564 |
\begin{itemize} |
\subsection{Building/compiling the code elsewhere} |
|
\item -rootdir=dir |
|
565 |
|
|
566 |
indicates where the model root directory is relative to the directory where |
In the example above (section \ref{sect:buildingCode}) we built the |
567 |
you are compiling. This option is not needed if you compile in the \textit{% |
executable in the {\em input} directory of the experiment for |
568 |
bin} directory (which is the default compilation directory) or within the |
convenience. You can also configure and compile the code in other |
569 |
\textit{verification} tree. |
locations, for example on a scratch disk with out having to copy the |
570 |
|
entire source tree. The only requirement to do so is you have {\tt |
571 |
|
genmake2} in your path or you know the absolute path to {\tt |
572 |
|
genmake2}. |
573 |
|
|
574 |
\item -mods=dir1,dir2,... |
The following sections outline some possible methods of organizing |
575 |
|
your source and data. |
576 |
|
|
577 |
indicates the relative or absolute paths directories where the sources |
\subsubsection{Building from the {\em ../code directory}} |
|
should take precedence over the default versions (located in \textit{model}, |
|
|
\textit{eesupp},...). Typically, this option is used when running the |
|
|
examples, see below. |
|
578 |
|
|
579 |
\item -enable=pkg1,pkg2,... |
This is just as simple as building in the {\em input/} directory: |
580 |
|
\begin{verbatim} |
581 |
|
% cd verification/exp2/code |
582 |
|
% ../../../tools/genmake2 |
583 |
|
% make depend |
584 |
|
% make |
585 |
|
\end{verbatim} |
586 |
|
However, to run the model the executable ({\em mitgcmuv}) and input |
587 |
|
files must be in the same place. If you only have one calculation to make: |
588 |
|
\begin{verbatim} |
589 |
|
% cd ../input |
590 |
|
% cp ../code/mitgcmuv ./ |
591 |
|
% ./mitgcmuv > output.txt |
592 |
|
\end{verbatim} |
593 |
|
or if you will be making multiple runs with the same executable: |
594 |
|
\begin{verbatim} |
595 |
|
% cd ../ |
596 |
|
% cp -r input run1 |
597 |
|
% cp code/mitgcmuv run1 |
598 |
|
% cd run1 |
599 |
|
% ./mitgcmuv > output.txt |
600 |
|
\end{verbatim} |
601 |
|
|
602 |
enables packages source code \textit{pkg1}, \textit{pkg2},... when creating |
\subsubsection{Building from a new directory} |
|
the makefile. |
|
603 |
|
|
604 |
\item -disable=pkg1,pkg2,... |
Since the {\em input} directory contains input files it is often more |
605 |
|
useful to keep {\em input} pristine and build in a new directory |
606 |
|
within {\em verification/exp2/}: |
607 |
|
\begin{verbatim} |
608 |
|
% cd verification/exp2 |
609 |
|
% mkdir build |
610 |
|
% cd build |
611 |
|
% ../../../tools/genmake2 -mods=../code |
612 |
|
% make depend |
613 |
|
% make |
614 |
|
\end{verbatim} |
615 |
|
This builds the code exactly as before but this time you need to copy |
616 |
|
either the executable or the input files or both in order to run the |
617 |
|
model. For example, |
618 |
|
\begin{verbatim} |
619 |
|
% cp ../input/* ./ |
620 |
|
% ./mitgcmuv > output.txt |
621 |
|
\end{verbatim} |
622 |
|
or if you tend to make multiple runs with the same executable then |
623 |
|
running in a new directory each time might be more appropriate: |
624 |
|
\begin{verbatim} |
625 |
|
% cd ../ |
626 |
|
% mkdir run1 |
627 |
|
% cp build/mitgcmuv run1/ |
628 |
|
% cp input/* run1/ |
629 |
|
% cd run1 |
630 |
|
% ./mitgcmuv > output.txt |
631 |
|
\end{verbatim} |
632 |
|
|
633 |
disables packages source code \textit{pkg1}, \textit{pkg2},... when creating |
\subsubsection{Building on a scratch disk} |
|
the makefile. |
|
634 |
|
|
635 |
\item -platform=machine |
Model object files and output data can use up large amounts of disk |
636 |
|
space so it is often the case that you will be operating on a large |
637 |
|
scratch disk. Assuming the model source is in {\em ~/MITgcm} then the |
638 |
|
following commands will build the model in {\em /scratch/exp2-run1}: |
639 |
|
\begin{verbatim} |
640 |
|
% cd /scratch/exp2-run1 |
641 |
|
% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ |
642 |
|
-mods=~/MITgcm/verification/exp2/code |
643 |
|
% make depend |
644 |
|
% make |
645 |
|
\end{verbatim} |
646 |
|
To run the model here, you'll need the input files: |
647 |
|
\begin{verbatim} |
648 |
|
% cp ~/MITgcm/verification/exp2/input/* ./ |
649 |
|
% ./mitgcmuv > output.txt |
650 |
|
\end{verbatim} |
651 |
|
|
652 |
specifies the platform for which you want the makefile. In general, you |
As before, you could build in one directory and make multiple runs of |
653 |
won't need this option. \textit{genmake} will select the right machine for |
the one experiment: |
654 |
you (the one you're working on!). However, this option is useful if you have |
\begin{verbatim} |
655 |
a choice of several compilers on one machine and you want to use the one |
% cd /scratch/exp2 |
656 |
that is not the default (ex: \texttt{pgf77} instead of \texttt{f77} under |
% mkdir build |
657 |
Linux). |
% cd build |
658 |
|
% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ |
659 |
|
-mods=~/MITgcm/verification/exp2/code |
660 |
|
% make depend |
661 |
|
% make |
662 |
|
% cd ../ |
663 |
|
% cp -r ~/MITgcm/verification/exp2/input run2 |
664 |
|
% cd run2 |
665 |
|
% ./mitgcmuv > output.txt |
666 |
|
\end{verbatim} |
667 |
|
|
|
\item -mpi |
|
668 |
|
|
|
this is used when you want to run the model in parallel processing mode |
|
|
under mpi (see section on parallel computation for more details). |
|
669 |
|
|
670 |
\item -jam |
\subsection{Using \textit{genmake2}} |
671 |
|
\label{sect:genmake} |
672 |
|
|
673 |
this is used when you want to run the model in parallel processing mode |
To compile the code, first use the program \texttt{genmake2} (located |
674 |
under jam (see section on parallel computation for more details). |
in the \textit{tools} directory) to generate a Makefile. |
675 |
\end{itemize} |
\texttt{genmake2} is a shell script written to work with all |
676 |
|
``sh''--compatible shells including bash v1, bash v2, and Bourne. |
677 |
|
Internally, \texttt{genmake2} determines the locations of needed |
678 |
|
files, the compiler, compiler options, libraries, and Unix tools. It |
679 |
|
relies upon a number of ``optfiles'' located in the {\em |
680 |
|
tools/build\_options} directory. |
681 |
|
|
682 |
|
The purpose of the optfiles is to provide all the compilation options |
683 |
|
for particular ``platforms'' (where ``platform'' roughly means the |
684 |
|
combination of the hardware and the compiler) and code configurations. |
685 |
|
Given the combinations of possible compilers and library dependencies |
686 |
|
({\it eg.} MPI and NetCDF) there may be numerous optfiles available |
687 |
|
for a single machine. The naming scheme for the majority of the |
688 |
|
optfiles shipped with the code is |
689 |
|
\begin{center} |
690 |
|
{\bf OS\_HARDWARE\_COMPILER } |
691 |
|
\end{center} |
692 |
|
where |
693 |
|
\begin{description} |
694 |
|
\item[OS] is the name of the operating system (generally the |
695 |
|
lower-case output of the {\tt 'uname'} command) |
696 |
|
\item[HARDWARE] is a string that describes the CPU type and |
697 |
|
corresponds to output from the {\tt 'uname -m'} command: |
698 |
|
\begin{description} |
699 |
|
\item[ia32] is for ``x86'' machines such as i386, i486, i586, i686, |
700 |
|
and athlon |
701 |
|
\item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2) |
702 |
|
\item[amd64] is AMD x86\_64 systems |
703 |
|
\item[ppc] is for Mac PowerPC systems |
704 |
|
\end{description} |
705 |
|
\item[COMPILER] is the compiler name (generally, the name of the |
706 |
|
FORTRAN executable) |
707 |
|
\end{description} |
708 |
|
|
709 |
|
In many cases, the default optfiles are sufficient and will result in |
710 |
|
usable Makefiles. However, for some machines or code configurations, |
711 |
|
new ``optfiles'' must be written. To create a new optfile, it is |
712 |
|
generally best to start with one of the defaults and modify it to suit |
713 |
|
your needs. Like \texttt{genmake2}, the optfiles are all written |
714 |
|
using a simple ``sh''--compatible syntax. While nearly all variables |
715 |
|
used within \texttt{genmake2} may be specified in the optfiles, the |
716 |
|
critical ones that should be defined are: |
717 |
|
|
718 |
|
\begin{description} |
719 |
|
\item[FC] the FORTRAN compiler (executable) to use |
720 |
|
\item[DEFINES] the command-line DEFINE options passed to the compiler |
721 |
|
\item[CPP] the C pre-processor to use |
722 |
|
\item[NOOPTFLAGS] options flags for special files that should not be |
723 |
|
optimized |
724 |
|
\end{description} |
725 |
|
|
726 |
For some of the examples, there is a file called \textit{.genmakerc} in the |
For example, the optfile for a typical Red Hat Linux machine (``ia32'' |
727 |
\textit{input} directory that has the relevant \textit{genmake} options for |
architecture) using the GCC (g77) compiler is |
|
that particular example. In this way you don't need to type the options when |
|
|
invoking \textit{genmake}. |
|
|
|
|
|
\subsubsection{Compiling} |
|
|
|
|
|
Let's assume that you want to run, say, example \textit{exp2} in the \textit{% |
|
|
input} directory. To compile the code, type the following commands from the |
|
|
model root tree: |
|
728 |
\begin{verbatim} |
\begin{verbatim} |
729 |
% cd verification/exp2/input |
FC=g77 |
730 |
% ../../../tools/genmake |
DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4' |
731 |
% make depend |
CPP='cpp -traditional -P' |
732 |
% make |
NOOPTFLAGS='-O0' |
733 |
|
# For IEEE, use the "-ffloat-store" option |
734 |
|
if test "x$IEEE" = x ; then |
735 |
|
FFLAGS='-Wimplicit -Wunused -Wuninitialized' |
736 |
|
FOPTIM='-O3 -malign-double -funroll-loops' |
737 |
|
else |
738 |
|
FFLAGS='-Wimplicit -Wunused -ffloat-store' |
739 |
|
FOPTIM='-O0 -malign-double' |
740 |
|
fi |
741 |
\end{verbatim} |
\end{verbatim} |
742 |
|
|
743 |
If there is no \textit{.genmakerc} in the \textit{input} directory, you have |
If you write an optfile for an unrepresented machine or compiler, you |
744 |
to use the following options when invoking \textit{genmake}: |
are strongly encouraged to submit the optfile to the MITgcm project |
745 |
\begin{verbatim} |
for inclusion. Please send the file to the |
746 |
% ../../../tools/genmake -mods=../code |
\begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml} |
747 |
\end{verbatim} |
\begin{center} |
748 |
|
MITgcm-support@mitgcm.org |
749 |
|
\end{center} |
750 |
|
\begin{rawhtml} </A> \end{rawhtml} |
751 |
|
mailing list. |
752 |
|
|
753 |
In addition, you will probably want to disable some of the packages. Taking |
In addition to the optfiles, \texttt{genmake2} supports a number of |
754 |
again the case of \textit{exp2}, the full \textit{genmake} command will |
helpful command-line options. A complete list of these options can be |
755 |
probably look like this: |
obtained from: |
756 |
\begin{verbatim} |
\begin{verbatim} |
757 |
% ../../../tools/genmake -mods=../code -disable=kpp,gmredi,aim,... |
% genmake2 -h |
758 |
\end{verbatim} |
\end{verbatim} |
759 |
|
|
760 |
The make command creates an executable called \textit{mitgcmuv}. |
The most important command-line options are: |
761 |
|
\begin{description} |
762 |
|
|
763 |
|
\item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that |
764 |
|
should be used for a particular build. |
765 |
|
|
766 |
|
If no "optfile" is specified (either through the command line or the |
767 |
|
MITGCM\_OPTFILE environment variable), genmake2 will try to make a |
768 |
|
reasonable guess from the list provided in {\em |
769 |
|
tools/build\_options}. The method used for making this guess is |
770 |
|
to first determine the combination of operating system and hardware |
771 |
|
(eg. "linux\_ia32") and then find a working FORTRAN compiler within |
772 |
|
the user's path. When these three items have been identified, |
773 |
|
genmake2 will try to find an optfile that has a matching name. |
774 |
|
|
775 |
|
\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file |
776 |
|
used for packages. |
777 |
|
|
778 |
|
If not specified, the default dependency file {\em pkg/pkg\_depend} |
779 |
|
is used. The syntax for this file is parsed on a line-by-line basis |
780 |
|
where each line containes either a comment ("\#") or a simple |
781 |
|
"PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol |
782 |
|
specifies a "must be used with" or a "must not be used with" |
783 |
|
relationship, respectively. If no rule is specified, then it is |
784 |
|
assumed that the two packages are compatible and will function |
785 |
|
either with or without each other. |
786 |
|
|
787 |
|
\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default |
788 |
|
set of packages to be used. |
789 |
|
|
790 |
|
If not set, the default package list will be read from {\em |
791 |
|
pkg/pkg\_default} |
792 |
|
|
793 |
|
\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or |
794 |
|
automatic differentiation options file to be used. The file is |
795 |
|
analogous to the ``optfile'' defined above but it specifies |
796 |
|
information for the AD build process. |
797 |
|
|
798 |
|
The default file is located in {\em |
799 |
|
tools/adjoint\_options/adjoint\_default} and it defines the "TAF" |
800 |
|
and "TAMC" compilers. An alternate version is also available at |
801 |
|
{\em tools/adjoint\_options/adjoint\_staf} that selects the newer |
802 |
|
"STAF" compiler. As with any compilers, it is helpful to have their |
803 |
|
directories listed in your {\tt \$PATH} environment variable. |
804 |
|
|
805 |
|
\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of |
806 |
|
directories containing ``modifications''. These directories contain |
807 |
|
files with names that may (or may not) exist in the main MITgcm |
808 |
|
source tree but will be overridden by any identically-named sources |
809 |
|
within the ``MODS'' directories. |
810 |
|
|
811 |
|
The order of precedence for this "name-hiding" is as follows: |
812 |
|
\begin{itemize} |
813 |
|
\item ``MODS'' directories (in the order given) |
814 |
|
\item Packages either explicitly specified or provided by default |
815 |
|
(in the order given) |
816 |
|
\item Packages included due to package dependencies (in the order |
817 |
|
that that package dependencies are parsed) |
818 |
|
\item The "standard dirs" (which may have been specified by the |
819 |
|
``-standarddirs'' option) |
820 |
|
\end{itemize} |
821 |
|
|
822 |
|
\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of |
823 |
|
soft-links and other bugs common with the \texttt{make} versions |
824 |
|
provided by commercial Unix vendors, GNU \texttt{make} (sometimes |
825 |
|
called \texttt{gmake}) should be preferred. This option provides a |
826 |
|
means for specifying the make executable to be used. |
827 |
|
|
828 |
|
\end{description} |
829 |
|
|
830 |
|
|
831 |
|
|
832 |
|
\section{Running the model} |
833 |
|
\label{sect:runModel} |
834 |
|
|
835 |
|
If compilation finished succesfuully (section \ref{sect:buildModel}) |
836 |
|
then an executable called {\em mitgcmuv} will now exist in the local |
837 |
|
directory. |
838 |
|
|
839 |
Note that you can compile and run the code in another directory than \textit{% |
To run the model as a single process (ie. not in parallel) simply |
840 |
input}. You just need to make sure that you copy the input data files into |
type: |
|
the directory where you want to run the model. For example to compile from |
|
|
\textit{code}: |
|
841 |
\begin{verbatim} |
\begin{verbatim} |
842 |
% cd verification/exp2/code |
% ./mitgcmuv |
843 |
% ../../../tools/genmake |
\end{verbatim} |
844 |
% make depend |
The ``./'' is a safe-guard to make sure you use the local executable |
845 |
% make |
in case you have others that exist in your path (surely odd if you |
846 |
|
do!). The above command will spew out many lines of text output to |
847 |
|
your screen. This output contains details such as parameter values as |
848 |
|
well as diagnostics such as mean Kinetic energy, largest CFL number, |
849 |
|
etc. It is worth keeping this text output with the binary output so we |
850 |
|
normally re-direct the {\em stdout} stream as follows: |
851 |
|
\begin{verbatim} |
852 |
|
% ./mitgcmuv > output.txt |
853 |
\end{verbatim} |
\end{verbatim} |
854 |
|
|
855 |
\subsection{Running the model} |
For the example experiments in {\em verification}, an example of the |
856 |
|
output is kept in {\em results/output.txt} for comparison. You can compare |
857 |
|
your {\em output.txt} with this one to check that the set-up works. |
858 |
|
|
859 |
|
|
|
The first thing to do is to run the code by typing \textit{mitgcmuv} and see |
|
|
what happens. You can compare what you get with what is in the \textit{% |
|
|
results} directory. Unless noted otherwise, most examples are set up to run |
|
|
for a few time steps only so that you can quickly figure out whether the |
|
|
model is working or not. |
|
860 |
|
|
861 |
\subsubsection{Output files} |
\subsection{Output files} |
862 |
|
|
863 |
The model produces various output files. At a minimum, the instantaneous |
The model produces various output files. At a minimum, the instantaneous |
864 |
``state'' of the model is written out, which is made of the following files: |
``state'' of the model is written out, which is made of the following files: |
909 |
used to restart the model but are overwritten every other time they are |
used to restart the model but are overwritten every other time they are |
910 |
output to save disk space during long integrations. |
output to save disk space during long integrations. |
911 |
|
|
912 |
\subsubsection{Looking at the output} |
\subsection{Looking at the output} |
913 |
|
|
914 |
All the model data are written according to a ``meta/data'' file format. |
All the model data are written according to a ``meta/data'' file format. |
915 |
Each variable is associated with two files with suffix names \textit{.data} |
Each variable is associated with two files with suffix names \textit{.data} |
923 |
\textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads |
\textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads |
924 |
the data. Look at the comments inside the script to see how to use it. |
the data. Look at the comments inside the script to see how to use it. |
925 |
|
|
926 |
\section{Code structure} |
Some examples of reading and visualizing some output in {\em Matlab}: |
927 |
|
\begin{verbatim} |
928 |
|
% matlab |
929 |
|
>> H=rdmds('Depth'); |
930 |
|
>> contourf(H');colorbar; |
931 |
|
>> title('Depth of fluid as used by model'); |
932 |
|
|
933 |
|
>> eta=rdmds('Eta',10); |
934 |
|
>> imagesc(eta');axis ij;colorbar; |
935 |
|
>> title('Surface height at iter=10'); |
936 |
|
|
937 |
|
>> eta=rdmds('Eta',[0:10:100]); |
938 |
|
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end |
939 |
|
\end{verbatim} |
940 |
|
|
941 |
\section{Doing it yourself: customizing the code} |
\section{Doing it yourself: customizing the code} |
942 |
|
|
|
\subsection{\protect\bigskip Configuration and setup} |
|
|
|
|
943 |
When you are ready to run the model in the configuration you want, the |
When you are ready to run the model in the configuration you want, the |
944 |
easiest thing is to use and adapt the setup of the case studies experiment |
easiest thing is to use and adapt the setup of the case studies |
945 |
(described previously) that is the closest to your configuration. Then, the |
experiment (described previously) that is the closest to your |
946 |
amount of setup will be minimized. In this section, we focus on the setup |
configuration. Then, the amount of setup will be minimized. In this |
947 |
relative to the ''numerical model'' part of the code (the setup relative to |
section, we focus on the setup relative to the ``numerical model'' |
948 |
the ''execution environment'' part is covered in the parallel implementation |
part of the code (the setup relative to the ``execution environment'' |
949 |
section) and on the variables and parameters that you are likely to change. |
part is covered in the parallel implementation section) and on the |
950 |
|
variables and parameters that you are likely to change. |
951 |
The CPP keys relative to the ''numerical model'' part of the code are all |
|
952 |
defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{% |
\subsection{Configuration and setup} |
953 |
model/inc }or in one of the \textit{code }directories of the case study |
|
954 |
experiments under \textit{verification.} The model parameters are defined |
The CPP keys relative to the ``numerical model'' part of the code are |
955 |
and declared in the file \textit{model/inc/PARAMS.h }and their default |
all defined and set in the file \textit{CPP\_OPTIONS.h }in the |
956 |
values are set in the routine \textit{model/src/set\_defaults.F. }The |
directory \textit{ model/inc }or in one of the \textit{code |
957 |
default values can be modified in the namelist file \textit{data }which |
}directories of the case study experiments under |
958 |
needs to be located in the directory where you will run the model. The |
\textit{verification.} The model parameters are defined and declared |
959 |
parameters are initialized in the routine \textit{model/src/ini\_parms.F}. |
in the file \textit{model/inc/PARAMS.h }and their default values are |
960 |
Look at this routine to see in what part of the namelist the parameters are |
set in the routine \textit{model/src/set\_defaults.F. }The default |
961 |
located. |
values can be modified in the namelist file \textit{data }which needs |
962 |
|
to be located in the directory where you will run the model. The |
963 |
In what follows the parameters are grouped into categories related to the |
parameters are initialized in the routine |
964 |
computational domain, the equations solved in the model, and the simulation |
\textit{model/src/ini\_parms.F}. Look at this routine to see in what |
965 |
controls. |
part of the namelist the parameters are located. |
966 |
|
|
967 |
\subsubsection{Computational domain, geometry and time-discretization} |
In what follows the parameters are grouped into categories related to |
968 |
|
the computational domain, the equations solved in the model, and the |
969 |
\begin{itemize} |
simulation controls. |
970 |
\item dimensions |
|
971 |
\end{itemize} |
\subsection{Computational domain, geometry and time-discretization} |
972 |
|
|
973 |
The number of points in the x, y,\textit{\ }and r\textit{\ }directions are |
\begin{description} |
974 |
represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }% |
\item[dimensions] \ |
975 |
and \textbf{Nr}\textit{\ }respectively which are declared and set in the |
|
976 |
file \textit{model/inc/SIZE.h. }(Again, this assumes a mono-processor |
The number of points in the x, y, and r directions are represented |
977 |
calculation. For multiprocessor calculations see section on parallel |
by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr} |
978 |
implementation.) |
respectively which are declared and set in the file |
979 |
|
\textit{model/inc/SIZE.h}. (Again, this assumes a mono-processor |
980 |
\begin{itemize} |
calculation. For multiprocessor calculations see the section on |
981 |
\item grid |
parallel implementation.) |
982 |
\end{itemize} |
|
983 |
|
\item[grid] \ |
984 |
Three different grids are available: cartesian, spherical polar, and |
|
985 |
curvilinear (including the cubed sphere). The grid is set through the |
Three different grids are available: cartesian, spherical polar, and |
986 |
logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{% |
curvilinear (which includes the cubed sphere). The grid is set |
987 |
usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{% |
through the logical variables \textbf{usingCartesianGrid}, |
988 |
usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear |
\textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}. |
989 |
grids, the southern boundary is defined through the variable \textbf{phiMin}% |
In the case of spherical and curvilinear grids, the southern |
990 |
\textit{\ }which corresponds to the latitude of the southern most cell face |
boundary is defined through the variable \textbf{phiMin} which |
991 |
(in degrees). The resolution along the x and y directions is controlled by |
corresponds to the latitude of the southern most cell face (in |
992 |
the 1D arrays \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters |
degrees). The resolution along the x and y directions is controlled |
993 |
in the case of a cartesian grid, in degrees otherwise). The vertical grid |
by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the |
994 |
spacing is set through the 1D array \textbf{delz }for the ocean (in meters) |
case of a cartesian grid, in degrees otherwise). The vertical grid |
995 |
or \textbf{delp}\textit{\ }for the atmosphere (in Pa). The variable \textbf{% |
spacing is set through the 1D array \textbf{delz} for the ocean (in |
996 |
Ro\_SeaLevel} represents the standard position of Sea-Level in ''R'' |
meters) or \textbf{delp} for the atmosphere (in Pa). The variable |
997 |
coordinate. This is typically set to 0m for the ocean (default value) and 10$% |
\textbf{Ro\_SeaLevel} represents the standard position of Sea-Level |
998 |
^{5}$Pa for the atmosphere. For the atmosphere, also set the logical |
in ``R'' coordinate. This is typically set to 0m for the ocean |
999 |
variable \textbf{groundAtK1} to '.\texttt{TRUE}.'. which put the first level |
(default value) and 10$^{5}$Pa for the atmosphere. For the |
1000 |
(k=1) at the lower boundary (ground). |
atmosphere, also set the logical variable \textbf{groundAtK1} to |
1001 |
|
\texttt{'.TRUE.'} which puts the first level (k=1) at the lower |
1002 |
For the cartesian grid case, the Coriolis parameter $f$ is set through the |
boundary (ground). |
1003 |
variables \textbf{f0}\textit{\ }and \textbf{beta}\textit{\ }which correspond |
|
1004 |
to the reference Coriolis parameter (in s$^{-1}$) and $\frac{\partial f}{% |
For the cartesian grid case, the Coriolis parameter $f$ is set |
1005 |
\partial y}$(in m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ }% |
through the variables \textbf{f0} and \textbf{beta} which correspond |
1006 |
is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the |
to the reference Coriolis parameter (in s$^{-1}$) and |
1007 |
southern edge of the domain. |
$\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively. |
1008 |
|
If \textbf{beta } is set to a nonzero value, \textbf{f0} is the |
1009 |
\begin{itemize} |
value of $f$ at the southern edge of the domain. |
1010 |
\item topography - full and partial cells |
|
1011 |
\end{itemize} |
\item[topography - full and partial cells] \ |
1012 |
|
|
1013 |
The domain bathymetry is read from a file that contains a 2D (x,y) map of |
The domain bathymetry is read from a file that contains a 2D (x,y) |
1014 |
depths (in m) for the ocean or pressures (in Pa) for the atmosphere. The |
map of depths (in m) for the ocean or pressures (in Pa) for the |
1015 |
file name is represented by the variable \textbf{bathyFile}\textit{. }The |
atmosphere. The file name is represented by the variable |
1016 |
file is assumed to contain binary numbers giving the depth (pressure) of the |
\textbf{bathyFile}. The file is assumed to contain binary numbers |
1017 |
model at each grid cell, ordered with the x coordinate varying fastest. The |
giving the depth (pressure) of the model at each grid cell, ordered |
1018 |
points are ordered from low coordinate to high coordinate for both axes. The |
with the x coordinate varying fastest. The points are ordered from |
1019 |
model code applies without modification to enclosed, periodic, and double |
low coordinate to high coordinate for both axes. The model code |
1020 |
periodic domains. Periodicity is assumed by default and is suppressed by |
applies without modification to enclosed, periodic, and double |
1021 |
setting the depths to 0m for the cells at the limits of the computational |
periodic domains. Periodicity is assumed by default and is |
1022 |
domain (note: not sure this is the case for the atmosphere). The precision |
suppressed by setting the depths to 0m for the cells at the limits |
1023 |
with which to read the binary data is controlled by the integer variable |
of the computational domain (note: not sure this is the case for the |
1024 |
\textbf{readBinaryPrec }which can take the value \texttt{32} (single |
atmosphere). The precision with which to read the binary data is |
1025 |
precision) or \texttt{64} (double precision). See the matlab program \textit{% |
controlled by the integer variable \textbf{readBinaryPrec} which can |
1026 |
gendata.m }in the \textit{input }directories under \textit{verification }to |
take the value \texttt{32} (single precision) or \texttt{64} (double |
1027 |
see how the bathymetry files are generated for the case study experiments. |
precision). See the matlab program \textit{gendata.m} in the |
1028 |
|
\textit{input} directories under \textit{verification} to see how |
1029 |
To use the partial cell capability, the variable \textbf{hFacMin}\textit{\ }% |
the bathymetry files are generated for the case study experiments. |
1030 |
needs to be set to a value between 0 and 1 (it is set to 1 by default) |
|
1031 |
corresponding to the minimum fractional size of the cell. For example if the |
To use the partial cell capability, the variable \textbf{hFacMin} |
1032 |
bottom cell is 500m thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the |
needs to be set to a value between 0 and 1 (it is set to 1 by |
1033 |
actual thickness of the cell (i.e. used in the code) can cover a range of |
default) corresponding to the minimum fractional size of the cell. |
1034 |
discrete values 50m apart from 50m to 500m depending on the value of the |
For example if the bottom cell is 500m thick and \textbf{hFacMin} is |
1035 |
bottom depth (in \textbf{bathyFile}) at this point. |
set to 0.1, the actual thickness of the cell (i.e. used in the code) |
1036 |
|
can cover a range of discrete values 50m apart from 50m to 500m |
1037 |
Note that the bottom depths (or pressures) need not coincide with the models |
depending on the value of the bottom depth (in \textbf{bathyFile}) |
1038 |
levels as deduced from \textbf{delz}\textit{\ }or\textit{\ }\textbf{delp}% |
at this point. |
1039 |
\textit{. }The model will interpolate the numbers in \textbf{bathyFile}% |
|
1040 |
\textit{\ }so that they match the levels obtained from \textbf{delz}\textit{% |
Note that the bottom depths (or pressures) need not coincide with |
1041 |
\ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. } |
the models levels as deduced from \textbf{delz} or \textbf{delp}. |
1042 |
|
The model will interpolate the numbers in \textbf{bathyFile} so that |
1043 |
(Note: the atmospheric case is a bit more complicated than what is written |
they match the levels obtained from \textbf{delz} or \textbf{delp} |
1044 |
here I think. To come soon...) |
and \textbf{hFacMin}. |
1045 |
|
|
1046 |
\begin{itemize} |
(Note: the atmospheric case is a bit more complicated than what is |
1047 |
\item time-discretization |
written here I think. To come soon...) |
1048 |
\end{itemize} |
|
1049 |
|
\item[time-discretization] \ |
1050 |
The time steps are set through the real variables \textbf{deltaTMom }and |
|
1051 |
\textbf{deltaTtracer }(in s) which represent the time step for the momentum |
The time steps are set through the real variables \textbf{deltaTMom} |
1052 |
and tracer equations, respectively. For synchronous integrations, simply set |
and \textbf{deltaTtracer} (in s) which represent the time step for |
1053 |
the two variables to the same value (or you can prescribe one time step only |
the momentum and tracer equations, respectively. For synchronous |
1054 |
through the variable \textbf{deltaT}). The Adams-Bashforth stabilizing |
integrations, simply set the two variables to the same value (or you |
1055 |
parameter is set through the variable \textbf{abEps }(dimensionless). The |
can prescribe one time step only through the variable |
1056 |
stagger baroclinic time stepping can be activated by setting the logical |
\textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set |
1057 |
variable \textbf{staggerTimeStep }to '.\texttt{TRUE}.'. |
through the variable \textbf{abEps} (dimensionless). The stagger |
1058 |
|
baroclinic time stepping can be activated by setting the logical |
1059 |
\subsubsection{Equation of state} |
variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}. |
1060 |
|
|
1061 |
First, because the model equations are written in terms of perturbations, a |
\end{description} |
1062 |
reference thermodynamic state needs to be specified. This is done through |
|
1063 |
the 1D arrays \textbf{tRef}\textit{\ }and \textbf{sRef}. \textbf{tRef }% |
|
1064 |
specifies the reference potential temperature profile (in $^{o}$C for |
\subsection{Equation of state} |
1065 |
the ocean and $^{o}$K for the atmosphere) starting from the level |
|
1066 |
k=1. Similarly, \textbf{sRef}\textit{\ }specifies the reference salinity |
First, because the model equations are written in terms of |
1067 |
profile (in ppt) for the ocean or the reference specific humidity profile |
perturbations, a reference thermodynamic state needs to be specified. |
1068 |
(in g/kg) for the atmosphere. |
This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}. |
1069 |
|
\textbf{tRef} specifies the reference potential temperature profile |
1070 |
The form of the equation of state is controlled by the character variables |
(in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting |
1071 |
\textbf{buoyancyRelation}\textit{\ }and \textbf{eosType}\textit{. }\textbf{% |
from the level k=1. Similarly, \textbf{sRef} specifies the reference |
1072 |
buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and |
salinity profile (in ppt) for the ocean or the reference specific |
1073 |
needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In |
humidity profile (in g/kg) for the atmosphere. |
1074 |
this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'. |
|
1075 |
For the ocean, two forms of the equation of state are available: linear (set |
The form of the equation of state is controlled by the character |
1076 |
\textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial |
variables \textbf{buoyancyRelation} and \textbf{eosType}. |
1077 |
approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\ |
\textbf{buoyancyRelation} is set to \texttt{'OCEANIC'} by default and |
1078 |
}to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the |
needs to be set to \texttt{'ATMOSPHERIC'} for atmosphere simulations. |
1079 |
thermal and haline expansion coefficients represented by the variables |
In this case, \textbf{eosType} must be set to \texttt{'IDEALGAS'}. |
1080 |
\textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(in ppt$% |
For the ocean, two forms of the equation of state are available: |
1081 |
^{-1}$). For the nonlinear case, you need to generate a file of polynomial |
linear (set \textbf{eosType} to \texttt{'LINEAR'}) and a polynomial |
1082 |
coefficients called \textit{POLY3.COEFFS. }To do this, use the program |
approximation to the full nonlinear equation ( set \textbf{eosType} to |
1083 |
\textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is |
\texttt{'POLYNOMIAL'}). In the linear case, you need to specify the |
1084 |
available in the same directory and you will need to edit the number and the |
thermal and haline expansion coefficients represented by the variables |
1085 |
values of the vertical levels in \textit{knudsen2.f }so that they match |
\textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For |
1086 |
those of your configuration). \textit{\ } |
the nonlinear case, you need to generate a file of polynomial |
1087 |
|
coefficients called \textit{POLY3.COEFFS}. To do this, use the program |
1088 |
\subsubsection{Momentum equations} |
\textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is |
1089 |
|
available in the same directory and you will need to edit the number |
1090 |
In this section, we only focus for now on the parameters that you are likely |
and the values of the vertical levels in \textit{knudsen2.f} so that |
1091 |
to change, i.e. the ones relative to forcing and dissipation for example. |
they match those of your configuration). |
1092 |
The details relevant to the vector-invariant form of the equations and the |
|
1093 |
various advection schemes are not covered for the moment. We assume that you |
There there are also higher polynomials for the equation of state: |
1094 |
use the standard form of the momentum equations (i.e. the flux-form) with |
\begin{description} |
1095 |
the default advection scheme. Also, there are a few logical variables that |
\item[\texttt{'UNESCO'}:] The UNESCO equation of state formula of |
1096 |
allow you to turn on/off various terms in the momentum equation. These |
Fofonoff and Millard \cite{fofonoff83}. This equation of state |
1097 |
variables are called \textbf{momViscosity, momAdvection, momForcing, |
assumes in-situ temperature, which is not a model variable; {\em its |
1098 |
useCoriolis, momPressureForcing, momStepping}\textit{, }and \textit{\ }% |
use is therefore discouraged, and it is only listed for |
1099 |
\textbf{metricTerms }and are assumed to be set to '.\texttt{TRUE}.' here. |
completeness}. |
1100 |
Look at the file \textit{model/inc/PARAMS.h }for a precise definition of |
\item[\texttt{'JMD95Z'}:] A modified UNESCO formula by Jackett and |
1101 |
these variables. |
McDougall \cite{jackett95}, which uses the model variable potential |
1102 |
|
temperature as input. The \texttt{'Z'} indicates that this equation |
1103 |
\begin{itemize} |
of state uses a horizontally and temporally constant pressure |
1104 |
\item initialization |
$p_{0}=-g\rho_{0}z$. |
1105 |
\end{itemize} |
\item[\texttt{'JMD95P'}:] A modified UNESCO formula by Jackett and |
1106 |
|
McDougall \cite{jackett95}, which uses the model variable potential |
1107 |
The velocity components are initialized to 0 unless the simulation is |
temperature as input. The \texttt{'P'} indicates that this equation |
1108 |
starting from a pickup file (see section on simulation control parameters). |
of state uses the actual hydrostatic pressure of the last time |
1109 |
|
step. Lagging the pressure in this way requires an additional pickup |
1110 |
\begin{itemize} |
file for restarts. |
1111 |
\item forcing |
\item[\texttt{'MDJWF'}:] The new, more accurate and less expensive |
1112 |
\end{itemize} |
equation of state by McDougall et~al. \cite{mcdougall03}. It also |
1113 |
|
requires lagging the pressure and therefore an additional pickup |
1114 |
This section only applies to the ocean. You need to generate wind-stress |
file for restarts. |
1115 |
data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{% |
\end{description} |
1116 |
meridWindFile }corresponding to the zonal and meridional components of the |
For none of these options an reference profile of temperature or |
1117 |
wind stress, respectively (if you want the stress to be along the direction |
salinity is required. |
1118 |
of only one of the model horizontal axes, you only need to generate one |
|
1119 |
file). The format of the files is similar to the bathymetry file. The zonal |
\subsection{Momentum equations} |
1120 |
(meridional) stress data are assumed to be in Pa and located at U-points |
|
1121 |
(V-points). As for the bathymetry, the precision with which to read the |
In this section, we only focus for now on the parameters that you are |
1122 |
binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } |
likely to change, i.e. the ones relative to forcing and dissipation |
1123 |
See the matlab program \textit{gendata.m }in the \textit{input }directories |
for example. The details relevant to the vector-invariant form of the |
1124 |
under \textit{verification }to see how simple analytical wind forcing data |
equations and the various advection schemes are not covered for the |
1125 |
are generated for the case study experiments. |
moment. We assume that you use the standard form of the momentum |
1126 |
|
equations (i.e. the flux-form) with the default advection scheme. |
1127 |
There is also the possibility of prescribing time-dependent periodic |
Also, there are a few logical variables that allow you to turn on/off |
1128 |
forcing. To do this, concatenate the successive time records into a single |
various terms in the momentum equation. These variables are called |
1129 |
file (for each stress component) ordered in a (x, y, t) fashion and set the |
\textbf{momViscosity, momAdvection, momForcing, useCoriolis, |
1130 |
following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.', |
momPressureForcing, momStepping} and \textbf{metricTerms }and are |
1131 |
\textbf{externForcingPeriod }to the period (in s) of which the forcing |
assumed to be set to \texttt{'.TRUE.'} here. Look at the file |
1132 |
varies (typically 1 month), and \textbf{externForcingCycle }to the repeat |
\textit{model/inc/PARAMS.h }for a precise definition of these |
1133 |
time (in s) of the forcing (typically 1 year -- note: \textbf{% |
variables. |
1134 |
externForcingCycle }must be a multiple of \textbf{externForcingPeriod}). |
|
1135 |
With these variables set up, the model will interpolate the forcing linearly |
\begin{description} |
1136 |
at each iteration. |
\item[initialization] \ |
1137 |
|
|
1138 |
\begin{itemize} |
The velocity components are initialized to 0 unless the simulation |
1139 |
\item dissipation |
is starting from a pickup file (see section on simulation control |
1140 |
\end{itemize} |
parameters). |
1141 |
|
|
1142 |
The lateral eddy viscosity coefficient is specified through the variable |
\item[forcing] \ |
1143 |
\textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity |
|
1144 |
coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$% |
This section only applies to the ocean. You need to generate |
1145 |
^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) |
wind-stress data into two files \textbf{zonalWindFile} and |
1146 |
for the atmosphere. The vertical diffusive fluxes can be computed implicitly |
\textbf{meridWindFile} corresponding to the zonal and meridional |
1147 |
by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}% |
components of the wind stress, respectively (if you want the stress |
1148 |
.'. In addition, biharmonic mixing can be added as well through the variable |
to be along the direction of only one of the model horizontal axes, |
1149 |
\textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid, |
you only need to generate one file). The format of the files is |
1150 |
you might also need to set the variable \textbf{cosPower} which is set to 0 |
similar to the bathymetry file. The zonal (meridional) stress data |
1151 |
by default and which represents the power of cosine of latitude to multiply |
are assumed to be in Pa and located at U-points (V-points). As for |
1152 |
viscosity. Slip or no-slip conditions at lateral and bottom boundaries are |
the bathymetry, the precision with which to read the binary data is |
1153 |
specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }% |
controlled by the variable \textbf{readBinaryPrec}. See the matlab |
1154 |
and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip |
program \textit{gendata.m} in the \textit{input} directories under |
1155 |
boundary conditions are applied. If no-slip boundary conditions are applied |
\textit{verification} to see how simple analytical wind forcing data |
1156 |
at the bottom, a bottom drag can be applied as well. Two forms are |
are generated for the case study experiments. |
1157 |
available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$% |
|
1158 |
^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{% |
There is also the possibility of prescribing time-dependent periodic |
1159 |
\ }in m$^{-1}$). |
forcing. To do this, concatenate the successive time records into a |
1160 |
|
single file (for each stress component) ordered in a (x,y,t) fashion |
1161 |
The Fourier and Shapiro filters are described elsewhere. |
and set the following variables: \textbf{periodicExternalForcing }to |
1162 |
|
\texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s) |
1163 |
\begin{itemize} |
of which the forcing varies (typically 1 month), and |
1164 |
\item C-D scheme |
\textbf{externForcingCycle} to the repeat time (in s) of the forcing |
1165 |
\end{itemize} |
(typically 1 year -- note: \textbf{ externForcingCycle} must be a |
1166 |
|
multiple of \textbf{externForcingPeriod}). With these variables set |
1167 |
If you run at a sufficiently coarse resolution, you will need the C-D scheme |
up, the model will interpolate the forcing linearly at each |
1168 |
for the computation of the Coriolis terms. The variable\textbf{\ tauCD}, |
iteration. |
1169 |
which represents the C-D scheme coupling timescale (in s) needs to be set. |
|
1170 |
|
\item[dissipation] \ |
1171 |
\begin{itemize} |
|
1172 |
\item calculation of pressure/geopotential |
The lateral eddy viscosity coefficient is specified through the |
1173 |
\end{itemize} |
variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy |
1174 |
|
viscosity coefficient is specified through the variable |
1175 |
First, to run a non-hydrostatic ocean simulation, set the logical variable |
\textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and |
1176 |
\textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure field is then |
\textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere. The |
1177 |
inverted through a 3D elliptic equation. (Note: this capability is not |
vertical diffusive fluxes can be computed implicitly by setting the |
1178 |
available for the atmosphere yet.) By default, a hydrostatic simulation is |
logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}. |
1179 |
assumed and a 2D elliptic equation is used to invert the pressure field. The |
In addition, biharmonic mixing can be added as well through the |
1180 |
parameters controlling the behaviour of the elliptic solvers are the |
variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar |
1181 |
variables \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual }% |
grid, you might also need to set the variable \textbf{cosPower} |
1182 |
for the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{% |
which is set to 0 by default and which represents the power of |
1183 |
cg3dTargetResidual }for the 3D case. You probably won't need to alter the |
cosine of latitude to multiply viscosity. Slip or no-slip conditions |
1184 |
default values (are we sure of this?). |
at lateral and bottom boundaries are specified through the logical |
1185 |
|
variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If |
1186 |
For the calculation of the surface pressure (for the ocean) or surface |
set to \texttt{'.FALSE.'}, free-slip boundary conditions are |
1187 |
geopotential (for the atmosphere) you need to set the logical variables |
applied. If no-slip boundary conditions are applied at the bottom, a |
1188 |
\textbf{rigidLid} and \textbf{implicitFreeSurface}\textit{\ }(set one to '.% |
bottom drag can be applied as well. Two forms are available: linear |
1189 |
\texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you |
(set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and |
1190 |
want to deal with the ocean upper or atmosphere lower boundary). |
quadratic (set the variable \textbf{bottomDragQuadratic} in |
1191 |
|
m$^{-1}$). |
1192 |
\subsubsection{Tracer equations} |
|
1193 |
|
The Fourier and Shapiro filters are described elsewhere. |
1194 |
This section covers the tracer equations i.e. the potential temperature |
|
1195 |
equation and the salinity (for the ocean) or specific humidity (for the |
\item[C-D scheme] \ |
1196 |
atmosphere) equation. As for the momentum equations, we only describe for |
|
1197 |
now the parameters that you are likely to change. The logical variables |
If you run at a sufficiently coarse resolution, you will need the |
1198 |
\textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{% |
C-D scheme for the computation of the Coriolis terms. The |
1199 |
tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off |
variable\textbf{\ tauCD}, which represents the C-D scheme coupling |
1200 |
terms in the temperature equation (same thing for salinity or specific |
timescale (in s) needs to be set. |
1201 |
humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{% |
|
1202 |
saltAdvection}\textit{\ }etc). These variables are all assumed here to be |
\item[calculation of pressure/geopotential] \ |
1203 |
set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a |
|
1204 |
precise definition. |
First, to run a non-hydrostatic ocean simulation, set the logical |
1205 |
|
variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure |
1206 |
\begin{itemize} |
field is then inverted through a 3D elliptic equation. (Note: this |
1207 |
\item initialization |
capability is not available for the atmosphere yet.) By default, a |
1208 |
\end{itemize} |
hydrostatic simulation is assumed and a 2D elliptic equation is used |
1209 |
|
to invert the pressure field. The parameters controlling the |
1210 |
The initial tracer data can be contained in the binary files \textbf{% |
behaviour of the elliptic solvers are the variables |
1211 |
hydrogThetaFile }and \textbf{hydrogSaltFile}. These files should contain 3D |
\textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for |
1212 |
data ordered in an (x, y, r) fashion with k=1 as the first vertical level. |
the 2D case and \textbf{cg3dMaxIters} and |
1213 |
If no file names are provided, the tracers are then initialized with the |
\textbf{cg3dTargetResidual} for the 3D case. You probably won't need to |
1214 |
values of \textbf{tRef }and \textbf{sRef }mentioned above (in the equation |
alter the default values (are we sure of this?). |
1215 |
of state section). In this case, the initial tracer data are uniform in x |
|
1216 |
and y for each depth level. |
For the calculation of the surface pressure (for the ocean) or |
1217 |
|
surface geopotential (for the atmosphere) you need to set the |
1218 |
\begin{itemize} |
logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface} |
1219 |
\item forcing |
(set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'} |
1220 |
\end{itemize} |
depending on how you want to deal with the ocean upper or atmosphere |
1221 |
|
lower boundary). |
1222 |
This part is more relevant for the ocean, the procedure for the atmosphere |
|
1223 |
not being completely stabilized at the moment. |
\end{description} |
1224 |
|
|
1225 |
A combination of fluxes data and relaxation terms can be used for driving |
\subsection{Tracer equations} |
1226 |
the tracer equations. \ For potential temperature, heat flux data (in W/m$% |
|
1227 |
^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }% |
This section covers the tracer equations i.e. the potential |
1228 |
Alternatively or in addition, the forcing can be specified through a |
temperature equation and the salinity (for the ocean) or specific |
1229 |
relaxation term. The SST data to which the model surface temperatures are |
humidity (for the atmosphere) equation. As for the momentum equations, |
1230 |
restored to are supposed to be stored in the 2D binary file \textbf{% |
we only describe for now the parameters that you are likely to change. |
1231 |
thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient |
The logical variables \textbf{tempDiffusion} \textbf{tempAdvection} |
1232 |
is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The |
\textbf{tempForcing}, and \textbf{tempStepping} allow you to turn |
1233 |
same procedure applies for salinity with the variable names \textbf{EmPmRfile% |
on/off terms in the temperature equation (same thing for salinity or |
1234 |
}\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}% |
specific humidity with variables \textbf{saltDiffusion}, |
1235 |
\textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data |
\textbf{saltAdvection} etc.). These variables are all assumed here to |
1236 |
files and relaxation time scale coefficient (in s), respectively. Also for |
be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h} |
1237 |
salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural |
for a precise definition. |
1238 |
boundary conditions are applied i.e. when computing the surface salinity |
|
1239 |
tendency, the freshwater flux is multiplied by the model surface salinity |
\begin{description} |
1240 |
instead of a constant salinity value. |
\item[initialization] \ |
1241 |
|
|
1242 |
As for the other input files, the precision with which to read the data is |
The initial tracer data can be contained in the binary files |
1243 |
controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic |
\textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files |
1244 |
forcing can be applied as well following the same procedure used for the |
should contain 3D data ordered in an (x,y,r) fashion with k=1 as the |
1245 |
wind forcing data (see above). |
first vertical level. If no file names are provided, the tracers |
1246 |
|
are then initialized with the values of \textbf{tRef} and |
1247 |
\begin{itemize} |
\textbf{sRef} mentioned above (in the equation of state section). In |
1248 |
\item dissipation |
this case, the initial tracer data are uniform in x and y for each |
1249 |
\end{itemize} |
depth level. |
1250 |
|
|
1251 |
Lateral eddy diffusivities for temperature and salinity/specific humidity |
\item[forcing] \ |
1252 |
are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }% |
|
1253 |
(in m$^{2}$/s). Vertical eddy diffusivities are specified through the |
This part is more relevant for the ocean, the procedure for the |
1254 |
variables \textbf{diffKzT }and \textbf{diffKzS }(in m$^{2}$/s) for the ocean |
atmosphere not being completely stabilized at the moment. |
1255 |
and \textbf{diffKpT }and \textbf{diffKpS }(in Pa$^{2}$/s) for the |
|
1256 |
atmosphere. The vertical diffusive fluxes can be computed implicitly by |
A combination of fluxes data and relaxation terms can be used for |
1257 |
setting the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}% |
driving the tracer equations. For potential temperature, heat flux |
1258 |
.'. In addition, biharmonic diffusivities can be specified as well through |
data (in W/m$ ^{2}$) can be stored in the 2D binary file |
1259 |
the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in m$^{4}$/s). Note |
\textbf{surfQfile}. Alternatively or in addition, the forcing can |
1260 |
that the cosine power scaling (specified through \textbf{cosPower }- see the |
be specified through a relaxation term. The SST data to which the |
1261 |
momentum equations section) is applied to the tracer diffusivities |
model surface temperatures are restored to are supposed to be stored |
1262 |
(Laplacian and biharmonic) as well. The Gent and McWilliams parameterization |
in the 2D binary file \textbf{thetaClimFile}. The corresponding |
1263 |
for oceanic tracers is described in the package section. Finally, note that |
relaxation time scale coefficient is set through the variable |
1264 |
tracers can be also subject to Fourier and Shapiro filtering (see the |
\textbf{tauThetaClimRelax} (in s). The same procedure applies for |
1265 |
corresponding section on these filters). |
salinity with the variable names \textbf{EmPmRfile}, |
1266 |
|
\textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater |
1267 |
\begin{itemize} |
flux (in m/s) and surface salinity (in ppt) data files and |
1268 |
\item ocean convection |
relaxation time scale coefficient (in s), respectively. Also for |
1269 |
\end{itemize} |
salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, |
1270 |
|
natural boundary conditions are applied i.e. when computing the |
1271 |
Two options are available to parameterize ocean convection: one is to use |
surface salinity tendency, the freshwater flux is multiplied by the |
1272 |
the convective adjustment scheme. In this case, you need to set the variable |
model surface salinity instead of a constant salinity value. |
1273 |
\textbf{cadjFreq}, which represents the frequency (in s) with which the |
|
1274 |
adjustment algorithm is called, to a non-zero value (if set to a negative |
As for the other input files, the precision with which to read the |
1275 |
value by the user, the model will set it to the tracer time step). The other |
data is controlled by the variable \textbf{readBinaryPrec}. |
1276 |
option is to parameterize convection with implicit vertical diffusion. To do |
Time-dependent, periodic forcing can be applied as well following |
1277 |
this, set the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}% |
the same procedure used for the wind forcing data (see above). |
1278 |
.' and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s) you |
|
1279 |
wish the tracer vertical diffusivities to have when mixing tracers |
\item[dissipation] \ |
1280 |
vertically due to static instabilities. Note that \textbf{cadjFreq }and |
|
1281 |
\textbf{ivdc\_kappa }can not both have non-zero value. |
Lateral eddy diffusivities for temperature and salinity/specific |
1282 |
|
humidity are specified through the variables \textbf{diffKhT} and |
1283 |
\subsubsection{Simulation controls} |
\textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are |
1284 |
|
specified through the variables \textbf{diffKzT} and |
1285 |
The model ''clock'' is defined by the variable \textbf{deltaTClock }(in s) |
\textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT |
1286 |
which determines the IO frequencies and is used in tagging output. |
}and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The |
1287 |
Typically, you will set it to the tracer time step for accelerated runs |
vertical diffusive fluxes can be computed implicitly by setting the |
1288 |
(otherwise it is simply set to the default time step \textbf{deltaT}). |
logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}. |
1289 |
Frequency of checkpointing and dumping of the model state are referenced to |
In addition, biharmonic diffusivities can be specified as well |
1290 |
this clock (see below). |
through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in |
1291 |
|
m$^{4}$/s). Note that the cosine power scaling (specified through |
1292 |
\begin{itemize} |
\textbf{cosPower}---see the momentum equations section) is applied to |
1293 |
\item run duration |
the tracer diffusivities (Laplacian and biharmonic) as well. The |
1294 |
\end{itemize} |
Gent and McWilliams parameterization for oceanic tracers is |
1295 |
|
described in the package section. Finally, note that tracers can be |
1296 |
The beginning of a simulation is set by specifying a start time (in s) |
also subject to Fourier and Shapiro filtering (see the corresponding |
1297 |
through the real variable \textbf{startTime }or by specifying an initial |
section on these filters). |
1298 |
iteration number through the integer variable \textbf{nIter0}. If these |
|
1299 |
variables are set to nonzero values, the model will look for a ''pickup'' |
\item[ocean convection] \ |
1300 |
file \textit{pickup.0000nIter0 }to restart the integration\textit{. }The end |
|
1301 |
of a simulation is set through the real variable \textbf{endTime }(in s). |
Two options are available to parameterize ocean convection: one is |
1302 |
Alternatively, you can specify instead the number of time steps to execute |
to use the convective adjustment scheme. In this case, you need to |
1303 |
through the integer variable \textbf{nTimeSteps}. |
set the variable \textbf{cadjFreq}, which represents the frequency |
1304 |
|
(in s) with which the adjustment algorithm is called, to a non-zero |
1305 |
\begin{itemize} |
value (if set to a negative value by the user, the model will set it |
1306 |
\item frequency of output |
to the tracer time step). The other option is to parameterize |
1307 |
\end{itemize} |
convection with implicit vertical diffusion. To do this, set the |
1308 |
|
logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'} |
1309 |
Real variables defining frequencies (in s) with which output files are |
and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s) |
1310 |
written on disk need to be set up. \textbf{dumpFreq }controls the frequency |
you wish the tracer vertical diffusivities to have when mixing |
1311 |
with which the instantaneous state of the model is saved. \textbf{chkPtFreq }% |
tracers vertically due to static instabilities. Note that |
1312 |
and \textbf{pchkPtFreq }control the output frequency of rolling and |
\textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero |
1313 |
permanent checkpoint files, respectively. See section 1.5.1 Output files for the |
value. |
1314 |
definition of model state and checkpoint files. In addition, time-averaged |
|
1315 |
fields can be written out by setting the variable \textbf{taveFreq} (in s). |
\end{description} |
1316 |
The precision with which to write the binary data is controlled by the |
|
1317 |
integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{% |
\subsection{Simulation controls} |
1318 |
64}). |
|
1319 |
|
The model ''clock'' is defined by the variable \textbf{deltaTClock} |
1320 |
|
(in s) which determines the IO frequencies and is used in tagging |
1321 |
|
output. Typically, you will set it to the tracer time step for |
1322 |
|
accelerated runs (otherwise it is simply set to the default time step |
1323 |
|
\textbf{deltaT}). Frequency of checkpointing and dumping of the model |
1324 |
|
state are referenced to this clock (see below). |
1325 |
|
|
1326 |
|
\begin{description} |
1327 |
|
\item[run duration] \ |
1328 |
|
|
1329 |
|
The beginning of a simulation is set by specifying a start time (in |
1330 |
|
s) through the real variable \textbf{startTime} or by specifying an |
1331 |
|
initial iteration number through the integer variable |
1332 |
|
\textbf{nIter0}. If these variables are set to nonzero values, the |
1333 |
|
model will look for a ''pickup'' file \textit{pickup.0000nIter0} to |
1334 |
|
restart the integration. The end of a simulation is set through the |
1335 |
|
real variable \textbf{endTime} (in s). Alternatively, you can |
1336 |
|
specify instead the number of time steps to execute through the |
1337 |
|
integer variable \textbf{nTimeSteps}. |
1338 |
|
|
1339 |
|
\item[frequency of output] \ |
1340 |
|
|
1341 |
|
Real variables defining frequencies (in s) with which output files |
1342 |
|
are written on disk need to be set up. \textbf{dumpFreq} controls |
1343 |
|
the frequency with which the instantaneous state of the model is |
1344 |
|
saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output |
1345 |
|
frequency of rolling and permanent checkpoint files, respectively. |
1346 |
|
See section 1.5.1 Output files for the definition of model state and |
1347 |
|
checkpoint files. In addition, time-averaged fields can be written |
1348 |
|
out by setting the variable \textbf{taveFreq} (in s). The precision |
1349 |
|
with which to write the binary data is controlled by the integer |
1350 |
|
variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or |
1351 |
|
\texttt{64}). |
1352 |
|
|
1353 |
|
\end{description} |
1354 |
|
|
1355 |
|
|
1356 |
|
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1357 |
|
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1358 |
|
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1359 |
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