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% $Header: /u/u3/gcmpack/manual/part3/getting_started.tex,v 1.20 2004/02/16 02:42:10 edhill Exp $ |
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% $Name: $ |
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|
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%\section{Getting started} |
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|
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In this section, we describe how to use the model. In the first |
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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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|
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\section{Where to find information} |
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\label{sect:whereToFindInfo} |
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|
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A web site is maintained for release 2 (``Pelican'') of MITgcm: |
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\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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|
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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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|
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|
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|
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\section{Obtaining the code} |
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\label{sect:obtainingCode} |
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|
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MITgcm can be downloaded from our system by following |
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the instructions below. As a courtesy we ask that you send e-mail to us at |
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\begin{rawhtml} <A href=mailto:MITgcm-support@mitgcm.org> \end{rawhtml} |
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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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|
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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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|
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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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|
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\end{enumerate} |
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|
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\subsubsection{Checkout from CVS} |
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\label{sect:cvs_checkout} |
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|
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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 |
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track of your changes. If CVS is not available on your machine, you can also |
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download a tar file. |
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|
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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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|
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|
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To get MITgcm through CVS, first register with the MITgcm CVS server |
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using command: |
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\begin{verbatim} |
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% cvs login ( CVS password: cvsanon ) |
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\end{verbatim} |
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You only need to do a ``cvs login'' once. |
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|
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To obtain the latest sources type: |
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\begin{verbatim} |
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% cvs co MITgcm |
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\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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|
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As a convenience, the MITgcm CVS server contains aliases which are |
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named subsets of the codebase. These aliases can be especially |
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helpful when used over slow internet connections or on machines with |
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restricted storage space. Table \ref{tab:cvsModules} contains a list |
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of CVS aliases |
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\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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|
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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} |
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% cvs co MITgcm_verif_basic |
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% mv MITgcm MITgcm_verif_basic |
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\end{verbatim} |
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|
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|
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\subsubsection{Conventional download method} |
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\label{sect:conventionalDownload} |
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|
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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} |
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http://mitgcm.org/download/ |
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\end{verbatim} |
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\begin{rawhtml} </A> \end{rawhtml} |
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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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us if you should need to send us your copy of the code. If a recent |
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tar file does not exist, then please contact the developers through |
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the |
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\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
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MITgcm-support@mitgcm.org |
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\begin{rawhtml} </A> \end{rawhtml} |
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mailing list. |
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|
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\subsubsection{Upgrading from an earlier version} |
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|
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If you already have an earlier version of the code you can ``upgrade'' |
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your copy instead of downloading the entire repository again. First, |
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``cd'' (change directory) to the top of your working copy: |
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\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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|
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\paragraph*{Upgrading to the current pre-release version} |
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|
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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: |
| 247 |
\begin{verbatim} |
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% cvs -q update -A -d -P |
| 249 |
\end{verbatim} |
| 250 |
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 |
| 252 |
very latest version. As a rule, we don't recommend this since you |
| 253 |
might upgrade while we are in the processes of checking in the code so |
| 254 |
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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|
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\section{Model and directory structure} |
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|
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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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|
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\begin{itemize} |
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|
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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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|
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\item \textit{diags}: contains the code relative to time-averaged |
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diagnostics. It is subdivided into two subdirectories \textit{inc} |
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and \textit{src} that contain include files (*.\textit{h} files) and |
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Fortran subroutines (*.\textit{F} files), respectively. |
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|
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\item \textit{doc}: contains brief documentation notes. |
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|
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\item \textit{eesupp}: contains the execution environment source code. |
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Also subdivided into two subdirectories \textit{inc} and |
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\textit{src}. |
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|
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\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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|
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\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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\textit{src}. |
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|
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\item \textit{pkg}: contains the source code for the packages. Each |
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package corresponds to a subdirectory. For example, \textit{gmredi} |
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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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physics. The packages are described in detail in section 3. |
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|
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\item \textit{tools}: this directory contains various useful tools. |
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For example, \textit{genmake2} is a script written in csh (C-shell) |
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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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|
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\item \textit{utils}: this directory contains various utilities. The |
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subdirectory \textit{knudsen2} contains code and a makefile that |
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compute coefficients of the polynomial approximation to the knudsen |
| 316 |
formula for an ocean nonlinear equation of state. The |
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\textit{matlab} subdirectory contains matlab scripts for reading |
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model output directly into matlab. \textit{scripts} contains C-shell |
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post-processing scripts for joining processor-based and tiled-based |
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model output. |
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|
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\item \textit{verification}: this directory contains the model |
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examples. See section \ref{sect:modelExamples}. |
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|
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\end{itemize} |
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|
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\section{Example experiments} |
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\label{sect:modelExamples} |
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|
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%% a set of twenty-four pre-configured numerical experiments |
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|
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The MITgcm distribution comes with more than a dozen pre-configured |
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numerical experiments. Some of these example experiments are tests of |
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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}. |
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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 |
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the directory \textit{verification}. Each example is briefly described |
| 341 |
below. |
| 342 |
|
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\subsection{Full list of model examples} |
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|
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\begin{enumerate} |
| 346 |
|
| 347 |
\item \textit{exp0} - single layer, ocean double gyre (barotropic with |
| 348 |
free-surface). This experiment is described in detail in section |
| 349 |
\ref{sect:eg-baro}. |
| 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 |
| 355 |
climatological forcing. This experiment is described in detail in |
| 356 |
section \ref{sect:eg-global}. |
| 357 |
|
| 358 |
\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{front\_relax} - Relaxation of an ocean thermal front (test for |
| 365 |
Gent/McWilliams scheme). 2D (Y-Z). |
| 366 |
|
| 367 |
\item \textit{internal wave} - Ocean internal wave forced by open |
| 368 |
boundary conditions. |
| 369 |
|
| 370 |
\item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP |
| 371 |
scheme; 1 month integration |
| 372 |
|
| 373 |
\item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and |
| 374 |
Suarez '94 forcing. |
| 375 |
|
| 376 |
\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and |
| 377 |
Suarez '94 forcing. |
| 378 |
|
| 379 |
\item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and |
| 380 |
Suarez '94 forcing on the cubed sphere. |
| 381 |
|
| 382 |
\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics. |
| 383 |
Global Zonal Mean configuration, 1x64x5 resolution. |
| 384 |
|
| 385 |
\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate |
| 386 |
Atmospheric physics, equatorial Slice configuration. 2D (X-Z). |
| 387 |
|
| 388 |
\item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric |
| 389 |
physics. 3D Equatorial Channel configuration. |
| 390 |
|
| 391 |
\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics. |
| 392 |
Global configuration, on latitude longitude grid with 128x64x5 grid |
| 393 |
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 |
\end{enumerate} |
| 429 |
|
| 430 |
\subsection{Directory structure of model examples} |
| 431 |
|
| 432 |
Each example directory has the following subdirectories: |
| 433 |
|
| 434 |
\begin{itemize} |
| 435 |
\item \textit{code}: contains the code particular to the example. At a |
| 436 |
minimum, this directory includes the following files: |
| 437 |
|
| 438 |
\begin{itemize} |
| 439 |
\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 |
On many systems, the {\em genmake2} program will be able to |
| 513 |
automatically recognize the hardware, find compilers and other tools |
| 514 |
within the user's path (``echo \$PATH''), and then choose an |
| 515 |
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 |
To specify an optfile to {\em genmake2}, the syntax is: |
| 533 |
\begin{verbatim} |
| 534 |
% ../../../tools/genmake2 -mods=../code -of /path/to/optfile |
| 535 |
\end{verbatim} |
| 536 |
|
| 537 |
Once a {\em Makefile} has been generated, we create the dependencies: |
| 538 |
\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 |
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 |
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 |
|
| 563 |
|
| 564 |
\subsection{Building/compiling the code elsewhere} |
| 565 |
|
| 566 |
In the example above (section \ref{sect:buildingCode}) we built the |
| 567 |
executable in the {\em input} directory of the experiment for |
| 568 |
convenience. You can also configure and compile the code in other |
| 569 |
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 |
The following sections outline some possible methods of organizing |
| 575 |
your source and data. |
| 576 |
|
| 577 |
\subsubsection{Building from the {\em ../code directory}} |
| 578 |
|
| 579 |
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 |
\subsubsection{Building from a new directory} |
| 603 |
|
| 604 |
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 |
\subsubsection{Building on a scratch disk} |
| 634 |
|
| 635 |
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 |
As before, you could build in one directory and make multiple runs of |
| 653 |
the one experiment: |
| 654 |
\begin{verbatim} |
| 655 |
% cd /scratch/exp2 |
| 656 |
% mkdir build |
| 657 |
% 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 |
|
| 668 |
|
| 669 |
|
| 670 |
\subsection{Using \textit{genmake2}} |
| 671 |
\label{sect:genmake} |
| 672 |
|
| 673 |
To compile the code, first use the program \texttt{genmake2} (located |
| 674 |
in the \textit{tools} directory) to generate a Makefile. |
| 675 |
\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 example, the optfile for a typical Red Hat Linux machine (``ia32'' |
| 727 |
architecture) using the GCC (g77) compiler is |
| 728 |
\begin{verbatim} |
| 729 |
FC=g77 |
| 730 |
DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4' |
| 731 |
CPP='cpp -traditional -P' |
| 732 |
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} |
| 742 |
|
| 743 |
If you write an optfile for an unrepresented machine or compiler, you |
| 744 |
are strongly encouraged to submit the optfile to the MITgcm project |
| 745 |
for inclusion. Please send the file to the |
| 746 |
\begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 747 |
\begin{center} |
| 748 |
MITgcm-support@mitgcm.org |
| 749 |
\end{center} |
| 750 |
\begin{rawhtml} </A> \end{rawhtml} |
| 751 |
mailing list. |
| 752 |
|
| 753 |
In addition to the optfiles, \texttt{genmake2} supports a number of |
| 754 |
helpful command-line options. A complete list of these options can be |
| 755 |
obtained from: |
| 756 |
\begin{verbatim} |
| 757 |
% genmake2 -h |
| 758 |
\end{verbatim} |
| 759 |
|
| 760 |
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 |
\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX) |
| 829 |
machines, the ``bash'' shell is unavailable. To run on these |
| 830 |
systems, \texttt{genmake2} can be invoked using an ``sh'' (that is, |
| 831 |
a Bourne, POSIX, or compatible) shell. The syntax in these |
| 832 |
circumstances is: |
| 833 |
\begin{center} |
| 834 |
\texttt{/bin/sh genmake2 -bash=/bin/sh [...options...]} |
| 835 |
\end{center} |
| 836 |
where \texttt{/bin/sh} can be replaced with the full path and name |
| 837 |
of the desired shell. |
| 838 |
|
| 839 |
\end{description} |
| 840 |
|
| 841 |
|
| 842 |
|
| 843 |
\section{Running the model} |
| 844 |
\label{sect:runModel} |
| 845 |
|
| 846 |
If compilation finished succesfuully (section \ref{sect:buildModel}) |
| 847 |
then an executable called {\em mitgcmuv} will now exist in the local |
| 848 |
directory. |
| 849 |
|
| 850 |
To run the model as a single process (ie. not in parallel) simply |
| 851 |
type: |
| 852 |
\begin{verbatim} |
| 853 |
% ./mitgcmuv |
| 854 |
\end{verbatim} |
| 855 |
The ``./'' is a safe-guard to make sure you use the local executable |
| 856 |
in case you have others that exist in your path (surely odd if you |
| 857 |
do!). The above command will spew out many lines of text output to |
| 858 |
your screen. This output contains details such as parameter values as |
| 859 |
well as diagnostics such as mean Kinetic energy, largest CFL number, |
| 860 |
etc. It is worth keeping this text output with the binary output so we |
| 861 |
normally re-direct the {\em stdout} stream as follows: |
| 862 |
\begin{verbatim} |
| 863 |
% ./mitgcmuv > output.txt |
| 864 |
\end{verbatim} |
| 865 |
|
| 866 |
For the example experiments in {\em verification}, an example of the |
| 867 |
output is kept in {\em results/output.txt} for comparison. You can compare |
| 868 |
your {\em output.txt} with this one to check that the set-up works. |
| 869 |
|
| 870 |
|
| 871 |
|
| 872 |
\subsection{Output files} |
| 873 |
|
| 874 |
The model produces various output files. At a minimum, the instantaneous |
| 875 |
``state'' of the model is written out, which is made of the following files: |
| 876 |
|
| 877 |
\begin{itemize} |
| 878 |
\item \textit{U.00000nIter} - zonal component of velocity field (m/s and $> |
| 879 |
0 $ eastward). |
| 880 |
|
| 881 |
\item \textit{V.00000nIter} - meridional component of velocity field (m/s |
| 882 |
and $> 0$ northward). |
| 883 |
|
| 884 |
\item \textit{W.00000nIter} - vertical component of velocity field (ocean: |
| 885 |
m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure |
| 886 |
i.e. downward). |
| 887 |
|
| 888 |
\item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C, |
| 889 |
atmosphere: $^{0}$K). |
| 890 |
|
| 891 |
\item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor |
| 892 |
(g/kg). |
| 893 |
|
| 894 |
\item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere: |
| 895 |
surface pressure anomaly (Pa). |
| 896 |
\end{itemize} |
| 897 |
|
| 898 |
The chain \textit{00000nIter} consists of ten figures that specify the |
| 899 |
iteration number at which the output is written out. For example, \textit{% |
| 900 |
U.0000000300} is the zonal velocity at iteration 300. |
| 901 |
|
| 902 |
In addition, a ``pickup'' or ``checkpoint'' file called: |
| 903 |
|
| 904 |
\begin{itemize} |
| 905 |
\item \textit{pickup.00000nIter} |
| 906 |
\end{itemize} |
| 907 |
|
| 908 |
is written out. This file represents the state of the model in a condensed |
| 909 |
form and is used for restarting the integration. If the C-D scheme is used, |
| 910 |
there is an additional ``pickup'' file: |
| 911 |
|
| 912 |
\begin{itemize} |
| 913 |
\item \textit{pickup\_cd.00000nIter} |
| 914 |
\end{itemize} |
| 915 |
|
| 916 |
containing the D-grid velocity data and that has to be written out as well |
| 917 |
in order to restart the integration. Rolling checkpoint files are the same |
| 918 |
as the pickup files but are named differently. Their name contain the chain |
| 919 |
\textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be |
| 920 |
used to restart the model but are overwritten every other time they are |
| 921 |
output to save disk space during long integrations. |
| 922 |
|
| 923 |
\subsection{Looking at the output} |
| 924 |
|
| 925 |
All the model data are written according to a ``meta/data'' file format. |
| 926 |
Each variable is associated with two files with suffix names \textit{.data} |
| 927 |
and \textit{.meta}. The \textit{.data} file contains the data written in |
| 928 |
binary form (big\_endian by default). The \textit{.meta} file is a |
| 929 |
``header'' file that contains information about the size and the structure |
| 930 |
of the \textit{.data} file. This way of organizing the output is |
| 931 |
particularly useful when running multi-processors calculations. The base |
| 932 |
version of the model includes a few matlab utilities to read output files |
| 933 |
written in this format. The matlab scripts are located in the directory |
| 934 |
\textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads |
| 935 |
the data. Look at the comments inside the script to see how to use it. |
| 936 |
|
| 937 |
Some examples of reading and visualizing some output in {\em Matlab}: |
| 938 |
\begin{verbatim} |
| 939 |
% matlab |
| 940 |
>> H=rdmds('Depth'); |
| 941 |
>> contourf(H');colorbar; |
| 942 |
>> title('Depth of fluid as used by model'); |
| 943 |
|
| 944 |
>> eta=rdmds('Eta',10); |
| 945 |
>> imagesc(eta');axis ij;colorbar; |
| 946 |
>> title('Surface height at iter=10'); |
| 947 |
|
| 948 |
>> eta=rdmds('Eta',[0:10:100]); |
| 949 |
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end |
| 950 |
\end{verbatim} |
| 951 |
|
| 952 |
\section{Doing it yourself: customizing the code} |
| 953 |
|
| 954 |
When you are ready to run the model in the configuration you want, the |
| 955 |
easiest thing is to use and adapt the setup of the case studies |
| 956 |
experiment (described previously) that is the closest to your |
| 957 |
configuration. Then, the amount of setup will be minimized. In this |
| 958 |
section, we focus on the setup relative to the ``numerical model'' |
| 959 |
part of the code (the setup relative to the ``execution environment'' |
| 960 |
part is covered in the parallel implementation section) and on the |
| 961 |
variables and parameters that you are likely to change. |
| 962 |
|
| 963 |
\subsection{Configuration and setup} |
| 964 |
|
| 965 |
The CPP keys relative to the ``numerical model'' part of the code are |
| 966 |
all defined and set in the file \textit{CPP\_OPTIONS.h }in the |
| 967 |
directory \textit{ model/inc }or in one of the \textit{code |
| 968 |
}directories of the case study experiments under |
| 969 |
\textit{verification.} The model parameters are defined and declared |
| 970 |
in the file \textit{model/inc/PARAMS.h }and their default values are |
| 971 |
set in the routine \textit{model/src/set\_defaults.F. }The default |
| 972 |
values can be modified in the namelist file \textit{data }which needs |
| 973 |
to be located in the directory where you will run the model. The |
| 974 |
parameters are initialized in the routine |
| 975 |
\textit{model/src/ini\_parms.F}. Look at this routine to see in what |
| 976 |
part of the namelist the parameters are located. |
| 977 |
|
| 978 |
In what follows the parameters are grouped into categories related to |
| 979 |
the computational domain, the equations solved in the model, and the |
| 980 |
simulation controls. |
| 981 |
|
| 982 |
\subsection{Computational domain, geometry and time-discretization} |
| 983 |
|
| 984 |
\begin{description} |
| 985 |
\item[dimensions] \ |
| 986 |
|
| 987 |
The number of points in the x, y, and r directions are represented |
| 988 |
by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr} |
| 989 |
respectively which are declared and set in the file |
| 990 |
\textit{model/inc/SIZE.h}. (Again, this assumes a mono-processor |
| 991 |
calculation. For multiprocessor calculations see the section on |
| 992 |
parallel implementation.) |
| 993 |
|
| 994 |
\item[grid] \ |
| 995 |
|
| 996 |
Three different grids are available: cartesian, spherical polar, and |
| 997 |
curvilinear (which includes the cubed sphere). The grid is set |
| 998 |
through the logical variables \textbf{usingCartesianGrid}, |
| 999 |
\textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}. |
| 1000 |
In the case of spherical and curvilinear grids, the southern |
| 1001 |
boundary is defined through the variable \textbf{phiMin} which |
| 1002 |
corresponds to the latitude of the southern most cell face (in |
| 1003 |
degrees). The resolution along the x and y directions is controlled |
| 1004 |
by the 1D arrays \textbf{delx} and \textbf{dely} (in meters in the |
| 1005 |
case of a cartesian grid, in degrees otherwise). The vertical grid |
| 1006 |
spacing is set through the 1D array \textbf{delz} for the ocean (in |
| 1007 |
meters) or \textbf{delp} for the atmosphere (in Pa). The variable |
| 1008 |
\textbf{Ro\_SeaLevel} represents the standard position of Sea-Level |
| 1009 |
in ``R'' coordinate. This is typically set to 0m for the ocean |
| 1010 |
(default value) and 10$^{5}$Pa for the atmosphere. For the |
| 1011 |
atmosphere, also set the logical variable \textbf{groundAtK1} to |
| 1012 |
\texttt{'.TRUE.'} which puts the first level (k=1) at the lower |
| 1013 |
boundary (ground). |
| 1014 |
|
| 1015 |
For the cartesian grid case, the Coriolis parameter $f$ is set |
| 1016 |
through the variables \textbf{f0} and \textbf{beta} which correspond |
| 1017 |
to the reference Coriolis parameter (in s$^{-1}$) and |
| 1018 |
$\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively. |
| 1019 |
If \textbf{beta } is set to a nonzero value, \textbf{f0} is the |
| 1020 |
value of $f$ at the southern edge of the domain. |
| 1021 |
|
| 1022 |
\item[topography - full and partial cells] \ |
| 1023 |
|
| 1024 |
The domain bathymetry is read from a file that contains a 2D (x,y) |
| 1025 |
map of depths (in m) for the ocean or pressures (in Pa) for the |
| 1026 |
atmosphere. The file name is represented by the variable |
| 1027 |
\textbf{bathyFile}. The file is assumed to contain binary numbers |
| 1028 |
giving the depth (pressure) of the model at each grid cell, ordered |
| 1029 |
with the x coordinate varying fastest. The points are ordered from |
| 1030 |
low coordinate to high coordinate for both axes. The model code |
| 1031 |
applies without modification to enclosed, periodic, and double |
| 1032 |
periodic domains. Periodicity is assumed by default and is |
| 1033 |
suppressed by setting the depths to 0m for the cells at the limits |
| 1034 |
of the computational domain (note: not sure this is the case for the |
| 1035 |
atmosphere). The precision with which to read the binary data is |
| 1036 |
controlled by the integer variable \textbf{readBinaryPrec} which can |
| 1037 |
take the value \texttt{32} (single precision) or \texttt{64} (double |
| 1038 |
precision). See the matlab program \textit{gendata.m} in the |
| 1039 |
\textit{input} directories under \textit{verification} to see how |
| 1040 |
the bathymetry files are generated for the case study experiments. |
| 1041 |
|
| 1042 |
To use the partial cell capability, the variable \textbf{hFacMin} |
| 1043 |
needs to be set to a value between 0 and 1 (it is set to 1 by |
| 1044 |
default) corresponding to the minimum fractional size of the cell. |
| 1045 |
For example if the bottom cell is 500m thick and \textbf{hFacMin} is |
| 1046 |
set to 0.1, the actual thickness of the cell (i.e. used in the code) |
| 1047 |
can cover a range of discrete values 50m apart from 50m to 500m |
| 1048 |
depending on the value of the bottom depth (in \textbf{bathyFile}) |
| 1049 |
at this point. |
| 1050 |
|
| 1051 |
Note that the bottom depths (or pressures) need not coincide with |
| 1052 |
the models levels as deduced from \textbf{delz} or \textbf{delp}. |
| 1053 |
The model will interpolate the numbers in \textbf{bathyFile} so that |
| 1054 |
they match the levels obtained from \textbf{delz} or \textbf{delp} |
| 1055 |
and \textbf{hFacMin}. |
| 1056 |
|
| 1057 |
(Note: the atmospheric case is a bit more complicated than what is |
| 1058 |
written here I think. To come soon...) |
| 1059 |
|
| 1060 |
\item[time-discretization] \ |
| 1061 |
|
| 1062 |
The time steps are set through the real variables \textbf{deltaTMom} |
| 1063 |
and \textbf{deltaTtracer} (in s) which represent the time step for |
| 1064 |
the momentum and tracer equations, respectively. For synchronous |
| 1065 |
integrations, simply set the two variables to the same value (or you |
| 1066 |
can prescribe one time step only through the variable |
| 1067 |
\textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set |
| 1068 |
through the variable \textbf{abEps} (dimensionless). The stagger |
| 1069 |
baroclinic time stepping can be activated by setting the logical |
| 1070 |
variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}. |
| 1071 |
|
| 1072 |
\end{description} |
| 1073 |
|
| 1074 |
|
| 1075 |
\subsection{Equation of state} |
| 1076 |
|
| 1077 |
First, because the model equations are written in terms of |
| 1078 |
perturbations, a reference thermodynamic state needs to be specified. |
| 1079 |
This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}. |
| 1080 |
\textbf{tRef} specifies the reference potential temperature profile |
| 1081 |
(in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting |
| 1082 |
from the level k=1. Similarly, \textbf{sRef} specifies the reference |
| 1083 |
salinity profile (in ppt) for the ocean or the reference specific |
| 1084 |
humidity profile (in g/kg) for the atmosphere. |
| 1085 |
|
| 1086 |
The form of the equation of state is controlled by the character |
| 1087 |
variables \textbf{buoyancyRelation} and \textbf{eosType}. |
| 1088 |
\textbf{buoyancyRelation} is set to \texttt{'OCEANIC'} by default and |
| 1089 |
needs to be set to \texttt{'ATMOSPHERIC'} for atmosphere simulations. |
| 1090 |
In this case, \textbf{eosType} must be set to \texttt{'IDEALGAS'}. |
| 1091 |
For the ocean, two forms of the equation of state are available: |
| 1092 |
linear (set \textbf{eosType} to \texttt{'LINEAR'}) and a polynomial |
| 1093 |
approximation to the full nonlinear equation ( set \textbf{eosType} to |
| 1094 |
\texttt{'POLYNOMIAL'}). In the linear case, you need to specify the |
| 1095 |
thermal and haline expansion coefficients represented by the variables |
| 1096 |
\textbf{tAlpha} (in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For |
| 1097 |
the nonlinear case, you need to generate a file of polynomial |
| 1098 |
coefficients called \textit{POLY3.COEFFS}. To do this, use the program |
| 1099 |
\textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is |
| 1100 |
available in the same directory and you will need to edit the number |
| 1101 |
and the values of the vertical levels in \textit{knudsen2.f} so that |
| 1102 |
they match those of your configuration). |
| 1103 |
|
| 1104 |
There there are also higher polynomials for the equation of state: |
| 1105 |
\begin{description} |
| 1106 |
\item[\texttt{'UNESCO'}:] The UNESCO equation of state formula of |
| 1107 |
Fofonoff and Millard \cite{fofonoff83}. This equation of state |
| 1108 |
assumes in-situ temperature, which is not a model variable; {\em its |
| 1109 |
use is therefore discouraged, and it is only listed for |
| 1110 |
completeness}. |
| 1111 |
\item[\texttt{'JMD95Z'}:] A modified UNESCO formula by Jackett and |
| 1112 |
McDougall \cite{jackett95}, which uses the model variable potential |
| 1113 |
temperature as input. The \texttt{'Z'} indicates that this equation |
| 1114 |
of state uses a horizontally and temporally constant pressure |
| 1115 |
$p_{0}=-g\rho_{0}z$. |
| 1116 |
\item[\texttt{'JMD95P'}:] A modified UNESCO formula by Jackett and |
| 1117 |
McDougall \cite{jackett95}, which uses the model variable potential |
| 1118 |
temperature as input. The \texttt{'P'} indicates that this equation |
| 1119 |
of state uses the actual hydrostatic pressure of the last time |
| 1120 |
step. Lagging the pressure in this way requires an additional pickup |
| 1121 |
file for restarts. |
| 1122 |
\item[\texttt{'MDJWF'}:] The new, more accurate and less expensive |
| 1123 |
equation of state by McDougall et~al. \cite{mcdougall03}. It also |
| 1124 |
requires lagging the pressure and therefore an additional pickup |
| 1125 |
file for restarts. |
| 1126 |
\end{description} |
| 1127 |
For none of these options an reference profile of temperature or |
| 1128 |
salinity is required. |
| 1129 |
|
| 1130 |
\subsection{Momentum equations} |
| 1131 |
|
| 1132 |
In this section, we only focus for now on the parameters that you are |
| 1133 |
likely to change, i.e. the ones relative to forcing and dissipation |
| 1134 |
for example. The details relevant to the vector-invariant form of the |
| 1135 |
equations and the various advection schemes are not covered for the |
| 1136 |
moment. We assume that you use the standard form of the momentum |
| 1137 |
equations (i.e. the flux-form) with the default advection scheme. |
| 1138 |
Also, there are a few logical variables that allow you to turn on/off |
| 1139 |
various terms in the momentum equation. These variables are called |
| 1140 |
\textbf{momViscosity, momAdvection, momForcing, useCoriolis, |
| 1141 |
momPressureForcing, momStepping} and \textbf{metricTerms }and are |
| 1142 |
assumed to be set to \texttt{'.TRUE.'} here. Look at the file |
| 1143 |
\textit{model/inc/PARAMS.h }for a precise definition of these |
| 1144 |
variables. |
| 1145 |
|
| 1146 |
\begin{description} |
| 1147 |
\item[initialization] \ |
| 1148 |
|
| 1149 |
The velocity components are initialized to 0 unless the simulation |
| 1150 |
is starting from a pickup file (see section on simulation control |
| 1151 |
parameters). |
| 1152 |
|
| 1153 |
\item[forcing] \ |
| 1154 |
|
| 1155 |
This section only applies to the ocean. You need to generate |
| 1156 |
wind-stress data into two files \textbf{zonalWindFile} and |
| 1157 |
\textbf{meridWindFile} corresponding to the zonal and meridional |
| 1158 |
components of the wind stress, respectively (if you want the stress |
| 1159 |
to be along the direction of only one of the model horizontal axes, |
| 1160 |
you only need to generate one file). The format of the files is |
| 1161 |
similar to the bathymetry file. The zonal (meridional) stress data |
| 1162 |
are assumed to be in Pa and located at U-points (V-points). As for |
| 1163 |
the bathymetry, the precision with which to read the binary data is |
| 1164 |
controlled by the variable \textbf{readBinaryPrec}. See the matlab |
| 1165 |
program \textit{gendata.m} in the \textit{input} directories under |
| 1166 |
\textit{verification} to see how simple analytical wind forcing data |
| 1167 |
are generated for the case study experiments. |
| 1168 |
|
| 1169 |
There is also the possibility of prescribing time-dependent periodic |
| 1170 |
forcing. To do this, concatenate the successive time records into a |
| 1171 |
single file (for each stress component) ordered in a (x,y,t) fashion |
| 1172 |
and set the following variables: \textbf{periodicExternalForcing }to |
| 1173 |
\texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s) |
| 1174 |
of which the forcing varies (typically 1 month), and |
| 1175 |
\textbf{externForcingCycle} to the repeat time (in s) of the forcing |
| 1176 |
(typically 1 year -- note: \textbf{ externForcingCycle} must be a |
| 1177 |
multiple of \textbf{externForcingPeriod}). With these variables set |
| 1178 |
up, the model will interpolate the forcing linearly at each |
| 1179 |
iteration. |
| 1180 |
|
| 1181 |
\item[dissipation] \ |
| 1182 |
|
| 1183 |
The lateral eddy viscosity coefficient is specified through the |
| 1184 |
variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy |
| 1185 |
viscosity coefficient is specified through the variable |
| 1186 |
\textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and |
| 1187 |
\textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere. The |
| 1188 |
vertical diffusive fluxes can be computed implicitly by setting the |
| 1189 |
logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}. |
| 1190 |
In addition, biharmonic mixing can be added as well through the |
| 1191 |
variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar |
| 1192 |
grid, you might also need to set the variable \textbf{cosPower} |
| 1193 |
which is set to 0 by default and which represents the power of |
| 1194 |
cosine of latitude to multiply viscosity. Slip or no-slip conditions |
| 1195 |
at lateral and bottom boundaries are specified through the logical |
| 1196 |
variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If |
| 1197 |
set to \texttt{'.FALSE.'}, free-slip boundary conditions are |
| 1198 |
applied. If no-slip boundary conditions are applied at the bottom, a |
| 1199 |
bottom drag can be applied as well. Two forms are available: linear |
| 1200 |
(set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and |
| 1201 |
quadratic (set the variable \textbf{bottomDragQuadratic} in |
| 1202 |
m$^{-1}$). |
| 1203 |
|
| 1204 |
The Fourier and Shapiro filters are described elsewhere. |
| 1205 |
|
| 1206 |
\item[C-D scheme] \ |
| 1207 |
|
| 1208 |
If you run at a sufficiently coarse resolution, you will need the |
| 1209 |
C-D scheme for the computation of the Coriolis terms. The |
| 1210 |
variable\textbf{\ tauCD}, which represents the C-D scheme coupling |
| 1211 |
timescale (in s) needs to be set. |
| 1212 |
|
| 1213 |
\item[calculation of pressure/geopotential] \ |
| 1214 |
|
| 1215 |
First, to run a non-hydrostatic ocean simulation, set the logical |
| 1216 |
variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure |
| 1217 |
field is then inverted through a 3D elliptic equation. (Note: this |
| 1218 |
capability is not available for the atmosphere yet.) By default, a |
| 1219 |
hydrostatic simulation is assumed and a 2D elliptic equation is used |
| 1220 |
to invert the pressure field. The parameters controlling the |
| 1221 |
behaviour of the elliptic solvers are the variables |
| 1222 |
\textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for |
| 1223 |
the 2D case and \textbf{cg3dMaxIters} and |
| 1224 |
\textbf{cg3dTargetResidual} for the 3D case. You probably won't need to |
| 1225 |
alter the default values (are we sure of this?). |
| 1226 |
|
| 1227 |
For the calculation of the surface pressure (for the ocean) or |
| 1228 |
surface geopotential (for the atmosphere) you need to set the |
| 1229 |
logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface} |
| 1230 |
(set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'} |
| 1231 |
depending on how you want to deal with the ocean upper or atmosphere |
| 1232 |
lower boundary). |
| 1233 |
|
| 1234 |
\end{description} |
| 1235 |
|
| 1236 |
\subsection{Tracer equations} |
| 1237 |
|
| 1238 |
This section covers the tracer equations i.e. the potential |
| 1239 |
temperature equation and the salinity (for the ocean) or specific |
| 1240 |
humidity (for the atmosphere) equation. As for the momentum equations, |
| 1241 |
we only describe for now the parameters that you are likely to change. |
| 1242 |
The logical variables \textbf{tempDiffusion} \textbf{tempAdvection} |
| 1243 |
\textbf{tempForcing}, and \textbf{tempStepping} allow you to turn |
| 1244 |
on/off terms in the temperature equation (same thing for salinity or |
| 1245 |
specific humidity with variables \textbf{saltDiffusion}, |
| 1246 |
\textbf{saltAdvection} etc.). These variables are all assumed here to |
| 1247 |
be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h} |
| 1248 |
for a precise definition. |
| 1249 |
|
| 1250 |
\begin{description} |
| 1251 |
\item[initialization] \ |
| 1252 |
|
| 1253 |
The initial tracer data can be contained in the binary files |
| 1254 |
\textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files |
| 1255 |
should contain 3D data ordered in an (x,y,r) fashion with k=1 as the |
| 1256 |
first vertical level. If no file names are provided, the tracers |
| 1257 |
are then initialized with the values of \textbf{tRef} and |
| 1258 |
\textbf{sRef} mentioned above (in the equation of state section). In |
| 1259 |
this case, the initial tracer data are uniform in x and y for each |
| 1260 |
depth level. |
| 1261 |
|
| 1262 |
\item[forcing] \ |
| 1263 |
|
| 1264 |
This part is more relevant for the ocean, the procedure for the |
| 1265 |
atmosphere not being completely stabilized at the moment. |
| 1266 |
|
| 1267 |
A combination of fluxes data and relaxation terms can be used for |
| 1268 |
driving the tracer equations. For potential temperature, heat flux |
| 1269 |
data (in W/m$ ^{2}$) can be stored in the 2D binary file |
| 1270 |
\textbf{surfQfile}. Alternatively or in addition, the forcing can |
| 1271 |
be specified through a relaxation term. The SST data to which the |
| 1272 |
model surface temperatures are restored to are supposed to be stored |
| 1273 |
in the 2D binary file \textbf{thetaClimFile}. The corresponding |
| 1274 |
relaxation time scale coefficient is set through the variable |
| 1275 |
\textbf{tauThetaClimRelax} (in s). The same procedure applies for |
| 1276 |
salinity with the variable names \textbf{EmPmRfile}, |
| 1277 |
\textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater |
| 1278 |
flux (in m/s) and surface salinity (in ppt) data files and |
| 1279 |
relaxation time scale coefficient (in s), respectively. Also for |
| 1280 |
salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, |
| 1281 |
natural boundary conditions are applied i.e. when computing the |
| 1282 |
surface salinity tendency, the freshwater flux is multiplied by the |
| 1283 |
model surface salinity instead of a constant salinity value. |
| 1284 |
|
| 1285 |
As for the other input files, the precision with which to read the |
| 1286 |
data is controlled by the variable \textbf{readBinaryPrec}. |
| 1287 |
Time-dependent, periodic forcing can be applied as well following |
| 1288 |
the same procedure used for the wind forcing data (see above). |
| 1289 |
|
| 1290 |
\item[dissipation] \ |
| 1291 |
|
| 1292 |
Lateral eddy diffusivities for temperature and salinity/specific |
| 1293 |
humidity are specified through the variables \textbf{diffKhT} and |
| 1294 |
\textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are |
| 1295 |
specified through the variables \textbf{diffKzT} and |
| 1296 |
\textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT |
| 1297 |
}and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The |
| 1298 |
vertical diffusive fluxes can be computed implicitly by setting the |
| 1299 |
logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}. |
| 1300 |
In addition, biharmonic diffusivities can be specified as well |
| 1301 |
through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in |
| 1302 |
m$^{4}$/s). Note that the cosine power scaling (specified through |
| 1303 |
\textbf{cosPower}---see the momentum equations section) is applied to |
| 1304 |
the tracer diffusivities (Laplacian and biharmonic) as well. The |
| 1305 |
Gent and McWilliams parameterization for oceanic tracers is |
| 1306 |
described in the package section. Finally, note that tracers can be |
| 1307 |
also subject to Fourier and Shapiro filtering (see the corresponding |
| 1308 |
section on these filters). |
| 1309 |
|
| 1310 |
\item[ocean convection] \ |
| 1311 |
|
| 1312 |
Two options are available to parameterize ocean convection: one is |
| 1313 |
to use the convective adjustment scheme. In this case, you need to |
| 1314 |
set the variable \textbf{cadjFreq}, which represents the frequency |
| 1315 |
(in s) with which the adjustment algorithm is called, to a non-zero |
| 1316 |
value (if set to a negative value by the user, the model will set it |
| 1317 |
to the tracer time step). The other option is to parameterize |
| 1318 |
convection with implicit vertical diffusion. To do this, set the |
| 1319 |
logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'} |
| 1320 |
and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s) |
| 1321 |
you wish the tracer vertical diffusivities to have when mixing |
| 1322 |
tracers vertically due to static instabilities. Note that |
| 1323 |
\textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero |
| 1324 |
value. |
| 1325 |
|
| 1326 |
\end{description} |
| 1327 |
|
| 1328 |
\subsection{Simulation controls} |
| 1329 |
|
| 1330 |
The model ''clock'' is defined by the variable \textbf{deltaTClock} |
| 1331 |
(in s) which determines the IO frequencies and is used in tagging |
| 1332 |
output. Typically, you will set it to the tracer time step for |
| 1333 |
accelerated runs (otherwise it is simply set to the default time step |
| 1334 |
\textbf{deltaT}). Frequency of checkpointing and dumping of the model |
| 1335 |
state are referenced to this clock (see below). |
| 1336 |
|
| 1337 |
\begin{description} |
| 1338 |
\item[run duration] \ |
| 1339 |
|
| 1340 |
The beginning of a simulation is set by specifying a start time (in |
| 1341 |
s) through the real variable \textbf{startTime} or by specifying an |
| 1342 |
initial iteration number through the integer variable |
| 1343 |
\textbf{nIter0}. If these variables are set to nonzero values, the |
| 1344 |
model will look for a ''pickup'' file \textit{pickup.0000nIter0} to |
| 1345 |
restart the integration. The end of a simulation is set through the |
| 1346 |
real variable \textbf{endTime} (in s). Alternatively, you can |
| 1347 |
specify instead the number of time steps to execute through the |
| 1348 |
integer variable \textbf{nTimeSteps}. |
| 1349 |
|
| 1350 |
\item[frequency of output] \ |
| 1351 |
|
| 1352 |
Real variables defining frequencies (in s) with which output files |
| 1353 |
are written on disk need to be set up. \textbf{dumpFreq} controls |
| 1354 |
the frequency with which the instantaneous state of the model is |
| 1355 |
saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output |
| 1356 |
frequency of rolling and permanent checkpoint files, respectively. |
| 1357 |
See section 1.5.1 Output files for the definition of model state and |
| 1358 |
checkpoint files. In addition, time-averaged fields can be written |
| 1359 |
out by setting the variable \textbf{taveFreq} (in s). The precision |
| 1360 |
with which to write the binary data is controlled by the integer |
| 1361 |
variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or |
| 1362 |
\texttt{64}). |
| 1363 |
|
| 1364 |
\end{description} |
| 1365 |
|
| 1366 |
|
| 1367 |
%%% Local Variables: |
| 1368 |
%%% mode: latex |
| 1369 |
%%% TeX-master: t |
| 1370 |
%%% End: |
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