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% $Header: /u/gcmpack/manual/part3/getting_started.tex,v 1.36 2006/06/27 19:08:22 molod 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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\begin{rawhtml} |
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<!-- CMIREDIR:whereToFindInfo: --> |
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\end{rawhtml} |
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|
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There is 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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|
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\section{Obtaining the code} |
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\label{sect:obtainingCode} |
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\begin{rawhtml} |
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<!-- CMIREDIR:obtainingCode: --> |
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\end{rawhtml} |
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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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\subsection{Method 1 - 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 \texttt{.cshrc} or \texttt{.tcshrc} file. For bash or sh |
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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 \texttt{MITgcm}. If |
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the directory \texttt{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 \texttt{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 \texttt{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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\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: |
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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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|
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\subsection{Method 2 - Tar file download} |
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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} |
| 232 |
\begin{rawhtml} </A> \end{rawhtml} |
| 233 |
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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\section{Model and directory structure} |
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\begin{rawhtml} |
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<!-- CMIREDIR:directory_structure: --> |
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\end{rawhtml} |
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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 |
| 251 |
model that uses the framework. Under this structure the model is split |
| 252 |
into execution environment support code and conventional numerical |
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model code. The execution environment support code is held under the |
| 254 |
\texttt{eesupp} directory. The grid point model code is held under the |
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\texttt{model} directory. Code execution actually starts in the |
| 256 |
\texttt{eesupp} routines and not in the \texttt{model} routines. For |
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this reason the top-level \texttt{MAIN.F} is in the |
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\texttt{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 \texttt{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 \texttt{doc}: contains brief documentation notes. |
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|
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\item \texttt{eesupp}: contains the execution environment source code. |
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Also subdivided into two subdirectories \texttt{inc} and |
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\texttt{src}. |
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|
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\item \texttt{model}: this directory contains the main source code. |
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Also subdivided into two subdirectories \texttt{inc} and |
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\texttt{src}. |
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|
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\item \texttt{pkg}: contains the source code for the packages. Each |
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package corresponds to a subdirectory. For example, \texttt{gmredi} |
| 279 |
contains the code related to the Gent-McWilliams/Redi scheme, |
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\texttt{aim} the code relative to the atmospheric intermediate |
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physics. The packages are described in detail in chapter \ref{chap.packagesI}. |
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|
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\item \texttt{tools}: this directory contains various useful tools. |
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For example, \texttt{genmake2} is a script written in csh (C-shell) |
| 285 |
that should be used to generate your makefile. The directory |
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\texttt{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 detail in part \ref{chap.ecco}. |
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This directory also contains the subdirectory build\_options, which |
| 290 |
contains the `optfiles' with the compiler options for the different |
| 291 |
compilers and machines that can run MITgcm. |
| 292 |
|
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\item \texttt{utils}: this directory contains various utilities. The |
| 294 |
subdirectory \texttt{knudsen2} contains code and a makefile that |
| 295 |
compute coefficients of the polynomial approximation to the knudsen |
| 296 |
formula for an ocean nonlinear equation of state. The |
| 297 |
\texttt{matlab} subdirectory contains matlab scripts for reading |
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model output directly into matlab. \texttt{scripts} contains C-shell |
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post-processing scripts for joining processor-based and tiled-based |
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model output. The subdirectory exch2 contains the code needed for |
| 301 |
the exch2 package to work with different combinations of domain |
| 302 |
decompositions. |
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|
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\item \texttt{verification}: this directory contains the model |
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examples. See section \ref{sect:modelExamples}. |
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|
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\item \texttt{jobs}: contains sample job scripts for running MITgcm. |
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|
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\item \texttt{lsopt}: Line search code used for optimization. |
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|
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\item \texttt{optim}: Interface between MITgcm and line search code. |
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|
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\end{itemize} |
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|
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\section[Building MITgcm]{Building the code} |
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\label{sect:buildingCode} |
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\begin{rawhtml} |
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<!-- CMIREDIR:buildingCode: --> |
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\end{rawhtml} |
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|
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To compile the code, we use the \texttt{make} program. This uses a |
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file (\texttt{Makefile}) that allows us to pre-process source files, |
| 323 |
specify compiler and optimization options and also figures out any |
| 324 |
file dependencies. We supply a script (\texttt{genmake2}), described |
| 325 |
in section \ref{sect:genmake}, that automatically creates the |
| 326 |
\texttt{Makefile} for you. You then need to build the dependencies and |
| 327 |
compile the code. |
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|
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As an example, assume that you want to build and run experiment |
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\texttt{verification/exp2}. The are multiple ways and places to |
| 331 |
actually do this but here let's build the code in |
| 332 |
\texttt{verification/exp2/build}: |
| 333 |
\begin{verbatim} |
| 334 |
% cd verification/exp2/build |
| 335 |
\end{verbatim} |
| 336 |
First, build the \texttt{Makefile}: |
| 337 |
\begin{verbatim} |
| 338 |
% ../../../tools/genmake2 -mods=../code |
| 339 |
\end{verbatim} |
| 340 |
The command line option tells \texttt{genmake} to override model source |
| 341 |
code with any files in the directory \texttt{../code/}. |
| 342 |
|
| 343 |
On many systems, the \texttt{genmake2} program will be able to |
| 344 |
automatically recognize the hardware, find compilers and other tools |
| 345 |
within the user's path (``\texttt{echo \$PATH}''), and then choose an |
| 346 |
appropriate set of options from the files (``optfiles'') contained in |
| 347 |
the \texttt{tools/build\_options} directory. Under some |
| 348 |
circumstances, a user may have to create a new ``optfile'' in order to |
| 349 |
specify the exact combination of compiler, compiler flags, libraries, |
| 350 |
and other options necessary to build a particular configuration of |
| 351 |
MITgcm. In such cases, it is generally helpful to read the existing |
| 352 |
``optfiles'' and mimic their syntax. |
| 353 |
|
| 354 |
Through the MITgcm-support list, the MITgcm developers are willing to |
| 355 |
provide help writing or modifing ``optfiles''. And we encourage users |
| 356 |
to post new ``optfiles'' (particularly ones for new machines or |
| 357 |
architectures) to the |
| 358 |
\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 359 |
MITgcm-support@mitgcm.org |
| 360 |
\begin{rawhtml} </A> \end{rawhtml} |
| 361 |
list. |
| 362 |
|
| 363 |
To specify an optfile to \texttt{genmake2}, the syntax is: |
| 364 |
\begin{verbatim} |
| 365 |
% ../../../tools/genmake2 -mods=../code -of /path/to/optfile |
| 366 |
\end{verbatim} |
| 367 |
|
| 368 |
Once a \texttt{Makefile} has been generated, we create the |
| 369 |
dependencies with the command: |
| 370 |
\begin{verbatim} |
| 371 |
% make depend |
| 372 |
\end{verbatim} |
| 373 |
This modifies the \texttt{Makefile} by attaching a (usually, long) |
| 374 |
list of files upon which other files depend. The purpose of this is to |
| 375 |
reduce re-compilation if and when you start to modify the code. The |
| 376 |
{\tt make depend} command also creates links from the model source to |
| 377 |
this directory. It is important to note that the {\tt make depend} |
| 378 |
stage will occasionally produce warnings or errors since the |
| 379 |
dependency parsing tool is unable to find all of the necessary header |
| 380 |
files (\textit{eg.} \texttt{netcdf.inc}). In these circumstances, it |
| 381 |
is usually OK to ignore the warnings/errors and proceed to the next |
| 382 |
step. |
| 383 |
|
| 384 |
Next one can compile the code using: |
| 385 |
\begin{verbatim} |
| 386 |
% make |
| 387 |
\end{verbatim} |
| 388 |
The {\tt make} command creates an executable called \texttt{mitgcmuv}. |
| 389 |
Additional make ``targets'' are defined within the makefile to aid in |
| 390 |
the production of adjoint and other versions of MITgcm. On SMP |
| 391 |
(shared multi-processor) systems, the build process can often be sped |
| 392 |
up appreciably using the command: |
| 393 |
\begin{verbatim} |
| 394 |
% make -j 2 |
| 395 |
\end{verbatim} |
| 396 |
where the ``2'' can be replaced with a number that corresponds to the |
| 397 |
number of CPUs available. |
| 398 |
|
| 399 |
Now you are ready to run the model. General instructions for doing so are |
| 400 |
given in section \ref{sect:runModel}. Here, we can run the model by |
| 401 |
first creating links to all the input files: |
| 402 |
\begin{verbatim} |
| 403 |
ln -s ../input/* . |
| 404 |
\end{verbatim} |
| 405 |
and then calling the executable with: |
| 406 |
\begin{verbatim} |
| 407 |
./mitgcmuv > output.txt |
| 408 |
\end{verbatim} |
| 409 |
where we are re-directing the stream of text output to the file |
| 410 |
\texttt{output.txt}. |
| 411 |
|
| 412 |
\subsection{Building/compiling the code elsewhere} |
| 413 |
|
| 414 |
In the example above (section \ref{sect:buildingCode}) we built the |
| 415 |
executable in the {\em input} directory of the experiment for |
| 416 |
convenience. You can also configure and compile the code in other |
| 417 |
locations, for example on a scratch disk with out having to copy the |
| 418 |
entire source tree. The only requirement to do so is you have {\tt |
| 419 |
genmake2} in your path or you know the absolute path to {\tt |
| 420 |
genmake2}. |
| 421 |
|
| 422 |
The following sections outline some possible methods of organizing |
| 423 |
your source and data. |
| 424 |
|
| 425 |
\subsubsection{Building from the {\em ../code directory}} |
| 426 |
|
| 427 |
This is just as simple as building in the {\em input/} directory: |
| 428 |
\begin{verbatim} |
| 429 |
% cd verification/exp2/code |
| 430 |
% ../../../tools/genmake2 |
| 431 |
% make depend |
| 432 |
% make |
| 433 |
\end{verbatim} |
| 434 |
However, to run the model the executable ({\em mitgcmuv}) and input |
| 435 |
files must be in the same place. If you only have one calculation to make: |
| 436 |
\begin{verbatim} |
| 437 |
% cd ../input |
| 438 |
% cp ../code/mitgcmuv ./ |
| 439 |
% ./mitgcmuv > output.txt |
| 440 |
\end{verbatim} |
| 441 |
or if you will be making multiple runs with the same executable: |
| 442 |
\begin{verbatim} |
| 443 |
% cd ../ |
| 444 |
% cp -r input run1 |
| 445 |
% cp code/mitgcmuv run1 |
| 446 |
% cd run1 |
| 447 |
% ./mitgcmuv > output.txt |
| 448 |
\end{verbatim} |
| 449 |
|
| 450 |
\subsubsection{Building from a new directory} |
| 451 |
|
| 452 |
Since the {\em input} directory contains input files it is often more |
| 453 |
useful to keep {\em input} pristine and build in a new directory |
| 454 |
within {\em verification/exp2/}: |
| 455 |
\begin{verbatim} |
| 456 |
% cd verification/exp2 |
| 457 |
% mkdir build |
| 458 |
% cd build |
| 459 |
% ../../../tools/genmake2 -mods=../code |
| 460 |
% make depend |
| 461 |
% make |
| 462 |
\end{verbatim} |
| 463 |
This builds the code exactly as before but this time you need to copy |
| 464 |
either the executable or the input files or both in order to run the |
| 465 |
model. For example, |
| 466 |
\begin{verbatim} |
| 467 |
% cp ../input/* ./ |
| 468 |
% ./mitgcmuv > output.txt |
| 469 |
\end{verbatim} |
| 470 |
or if you tend to make multiple runs with the same executable then |
| 471 |
running in a new directory each time might be more appropriate: |
| 472 |
\begin{verbatim} |
| 473 |
% cd ../ |
| 474 |
% mkdir run1 |
| 475 |
% cp build/mitgcmuv run1/ |
| 476 |
% cp input/* run1/ |
| 477 |
% cd run1 |
| 478 |
% ./mitgcmuv > output.txt |
| 479 |
\end{verbatim} |
| 480 |
|
| 481 |
\subsubsection{Building on a scratch disk} |
| 482 |
|
| 483 |
Model object files and output data can use up large amounts of disk |
| 484 |
space so it is often the case that you will be operating on a large |
| 485 |
scratch disk. Assuming the model source is in {\em ~/MITgcm} then the |
| 486 |
following commands will build the model in {\em /scratch/exp2-run1}: |
| 487 |
\begin{verbatim} |
| 488 |
% cd /scratch/exp2-run1 |
| 489 |
% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ |
| 490 |
-mods=~/MITgcm/verification/exp2/code |
| 491 |
% make depend |
| 492 |
% make |
| 493 |
\end{verbatim} |
| 494 |
To run the model here, you'll need the input files: |
| 495 |
\begin{verbatim} |
| 496 |
% cp ~/MITgcm/verification/exp2/input/* ./ |
| 497 |
% ./mitgcmuv > output.txt |
| 498 |
\end{verbatim} |
| 499 |
|
| 500 |
As before, you could build in one directory and make multiple runs of |
| 501 |
the one experiment: |
| 502 |
\begin{verbatim} |
| 503 |
% cd /scratch/exp2 |
| 504 |
% mkdir build |
| 505 |
% cd build |
| 506 |
% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ |
| 507 |
-mods=~/MITgcm/verification/exp2/code |
| 508 |
% make depend |
| 509 |
% make |
| 510 |
% cd ../ |
| 511 |
% cp -r ~/MITgcm/verification/exp2/input run2 |
| 512 |
% cd run2 |
| 513 |
% ./mitgcmuv > output.txt |
| 514 |
\end{verbatim} |
| 515 |
|
| 516 |
|
| 517 |
\subsection{Using \texttt{genmake2}} |
| 518 |
\label{sect:genmake} |
| 519 |
|
| 520 |
To compile the code, first use the program \texttt{genmake2} (located |
| 521 |
in the \texttt{tools} directory) to generate a Makefile. |
| 522 |
\texttt{genmake2} is a shell script written to work with all |
| 523 |
``sh''--compatible shells including bash v1, bash v2, and Bourne. |
| 524 |
Internally, \texttt{genmake2} determines the locations of needed |
| 525 |
files, the compiler, compiler options, libraries, and Unix tools. It |
| 526 |
relies upon a number of ``optfiles'' located in the |
| 527 |
\texttt{tools/build\_options} directory. |
| 528 |
|
| 529 |
The purpose of the optfiles is to provide all the compilation options |
| 530 |
for particular ``platforms'' (where ``platform'' roughly means the |
| 531 |
combination of the hardware and the compiler) and code configurations. |
| 532 |
Given the combinations of possible compilers and library dependencies |
| 533 |
({\it eg.} MPI and NetCDF) there may be numerous optfiles available |
| 534 |
for a single machine. The naming scheme for the majority of the |
| 535 |
optfiles shipped with the code is |
| 536 |
\begin{center} |
| 537 |
{\bf OS\_HARDWARE\_COMPILER } |
| 538 |
\end{center} |
| 539 |
where |
| 540 |
\begin{description} |
| 541 |
\item[OS] is the name of the operating system (generally the |
| 542 |
lower-case output of the {\tt 'uname'} command) |
| 543 |
\item[HARDWARE] is a string that describes the CPU type and |
| 544 |
corresponds to output from the {\tt 'uname -m'} command: |
| 545 |
\begin{description} |
| 546 |
\item[ia32] is for ``x86'' machines such as i386, i486, i586, i686, |
| 547 |
and athlon |
| 548 |
\item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2) |
| 549 |
\item[amd64] is AMD x86\_64 systems |
| 550 |
\item[ppc] is for Mac PowerPC systems |
| 551 |
\end{description} |
| 552 |
\item[COMPILER] is the compiler name (generally, the name of the |
| 553 |
FORTRAN executable) |
| 554 |
\end{description} |
| 555 |
|
| 556 |
In many cases, the default optfiles are sufficient and will result in |
| 557 |
usable Makefiles. However, for some machines or code configurations, |
| 558 |
new ``optfiles'' must be written. To create a new optfile, it is |
| 559 |
generally best to start with one of the defaults and modify it to suit |
| 560 |
your needs. Like \texttt{genmake2}, the optfiles are all written |
| 561 |
using a simple ``sh''--compatible syntax. While nearly all variables |
| 562 |
used within \texttt{genmake2} may be specified in the optfiles, the |
| 563 |
critical ones that should be defined are: |
| 564 |
|
| 565 |
\begin{description} |
| 566 |
\item[FC] the FORTRAN compiler (executable) to use |
| 567 |
\item[DEFINES] the command-line DEFINE options passed to the compiler |
| 568 |
\item[CPP] the C pre-processor to use |
| 569 |
\item[NOOPTFLAGS] options flags for special files that should not be |
| 570 |
optimized |
| 571 |
\end{description} |
| 572 |
|
| 573 |
For example, the optfile for a typical Red Hat Linux machine (``ia32'' |
| 574 |
architecture) using the GCC (g77) compiler is |
| 575 |
\begin{verbatim} |
| 576 |
FC=g77 |
| 577 |
DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4' |
| 578 |
CPP='cpp -traditional -P' |
| 579 |
NOOPTFLAGS='-O0' |
| 580 |
# For IEEE, use the "-ffloat-store" option |
| 581 |
if test "x$IEEE" = x ; then |
| 582 |
FFLAGS='-Wimplicit -Wunused -Wuninitialized' |
| 583 |
FOPTIM='-O3 -malign-double -funroll-loops' |
| 584 |
else |
| 585 |
FFLAGS='-Wimplicit -Wunused -ffloat-store' |
| 586 |
FOPTIM='-O0 -malign-double' |
| 587 |
fi |
| 588 |
\end{verbatim} |
| 589 |
|
| 590 |
If you write an optfile for an unrepresented machine or compiler, you |
| 591 |
are strongly encouraged to submit the optfile to the MITgcm project |
| 592 |
for inclusion. Please send the file to the |
| 593 |
\begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 594 |
\begin{center} |
| 595 |
MITgcm-support@mitgcm.org |
| 596 |
\end{center} |
| 597 |
\begin{rawhtml} </A> \end{rawhtml} |
| 598 |
mailing list. |
| 599 |
|
| 600 |
In addition to the optfiles, \texttt{genmake2} supports a number of |
| 601 |
helpful command-line options. A complete list of these options can be |
| 602 |
obtained from: |
| 603 |
\begin{verbatim} |
| 604 |
% genmake2 -h |
| 605 |
\end{verbatim} |
| 606 |
|
| 607 |
The most important command-line options are: |
| 608 |
\begin{description} |
| 609 |
|
| 610 |
\item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that |
| 611 |
should be used for a particular build. |
| 612 |
|
| 613 |
If no "optfile" is specified (either through the command line or the |
| 614 |
MITGCM\_OPTFILE environment variable), genmake2 will try to make a |
| 615 |
reasonable guess from the list provided in {\em |
| 616 |
tools/build\_options}. The method used for making this guess is |
| 617 |
to first determine the combination of operating system and hardware |
| 618 |
(eg. "linux\_ia32") and then find a working FORTRAN compiler within |
| 619 |
the user's path. When these three items have been identified, |
| 620 |
genmake2 will try to find an optfile that has a matching name. |
| 621 |
|
| 622 |
\item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default |
| 623 |
set of packages to be used. The normal order of precedence for |
| 624 |
packages is as follows: |
| 625 |
\begin{enumerate} |
| 626 |
\item If available, the command line (\texttt{--pdefault}) settings |
| 627 |
over-rule any others. |
| 628 |
|
| 629 |
\item Next, \texttt{genmake2} will look for a file named |
| 630 |
``\texttt{packages.conf}'' in the local directory or in any of the |
| 631 |
directories specified with the \texttt{--mods} option. |
| 632 |
|
| 633 |
\item Finally, if neither of the above are available, |
| 634 |
\texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file. |
| 635 |
\end{enumerate} |
| 636 |
|
| 637 |
\item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file |
| 638 |
used for packages. |
| 639 |
|
| 640 |
If not specified, the default dependency file {\em pkg/pkg\_depend} |
| 641 |
is used. The syntax for this file is parsed on a line-by-line basis |
| 642 |
where each line containes either a comment ("\#") or a simple |
| 643 |
"PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol |
| 644 |
specifies a "must be used with" or a "must not be used with" |
| 645 |
relationship, respectively. If no rule is specified, then it is |
| 646 |
assumed that the two packages are compatible and will function |
| 647 |
either with or without each other. |
| 648 |
|
| 649 |
\item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or |
| 650 |
automatic differentiation options file to be used. The file is |
| 651 |
analogous to the ``optfile'' defined above but it specifies |
| 652 |
information for the AD build process. |
| 653 |
|
| 654 |
The default file is located in {\em |
| 655 |
tools/adjoint\_options/adjoint\_default} and it defines the "TAF" |
| 656 |
and "TAMC" compilers. An alternate version is also available at |
| 657 |
{\em tools/adjoint\_options/adjoint\_staf} that selects the newer |
| 658 |
"STAF" compiler. As with any compilers, it is helpful to have their |
| 659 |
directories listed in your {\tt \$PATH} environment variable. |
| 660 |
|
| 661 |
\item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of |
| 662 |
directories containing ``modifications''. These directories contain |
| 663 |
files with names that may (or may not) exist in the main MITgcm |
| 664 |
source tree but will be overridden by any identically-named sources |
| 665 |
within the ``MODS'' directories. |
| 666 |
|
| 667 |
The order of precedence for this "name-hiding" is as follows: |
| 668 |
\begin{itemize} |
| 669 |
\item ``MODS'' directories (in the order given) |
| 670 |
\item Packages either explicitly specified or provided by default |
| 671 |
(in the order given) |
| 672 |
\item Packages included due to package dependencies (in the order |
| 673 |
that that package dependencies are parsed) |
| 674 |
\item The "standard dirs" (which may have been specified by the |
| 675 |
``-standarddirs'' option) |
| 676 |
\end{itemize} |
| 677 |
|
| 678 |
\item[\texttt{--mpi}] This option enables certain MPI features (using |
| 679 |
CPP \texttt{\#define}s) within the code and is necessary for MPI |
| 680 |
builds (see Section \ref{sect:mpi-build}). |
| 681 |
|
| 682 |
\item[\texttt{--make=/path/to/gmake}] Due to the poor handling of |
| 683 |
soft-links and other bugs common with the \texttt{make} versions |
| 684 |
provided by commercial Unix vendors, GNU \texttt{make} (sometimes |
| 685 |
called \texttt{gmake}) should be preferred. This option provides a |
| 686 |
means for specifying the make executable to be used. |
| 687 |
|
| 688 |
\item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX) |
| 689 |
machines, the ``bash'' shell is unavailable. To run on these |
| 690 |
systems, \texttt{genmake2} can be invoked using an ``sh'' (that is, |
| 691 |
a Bourne, POSIX, or compatible) shell. The syntax in these |
| 692 |
circumstances is: |
| 693 |
\begin{center} |
| 694 |
\texttt{\% /bin/sh genmake2 -bash=/bin/sh [...options...]} |
| 695 |
\end{center} |
| 696 |
where \texttt{/bin/sh} can be replaced with the full path and name |
| 697 |
of the desired shell. |
| 698 |
|
| 699 |
\end{description} |
| 700 |
|
| 701 |
|
| 702 |
\subsection{Building with MPI} |
| 703 |
\label{sect:mpi-build} |
| 704 |
|
| 705 |
Building MITgcm to use MPI libraries can be complicated due to the |
| 706 |
variety of different MPI implementations available, their dependencies |
| 707 |
or interactions with different compilers, and their often ad-hoc |
| 708 |
locations within file systems. For these reasons, its generally a |
| 709 |
good idea to start by finding and reading the documentation for your |
| 710 |
machine(s) and, if necessary, seeking help from your local systems |
| 711 |
administrator. |
| 712 |
|
| 713 |
The steps for building MITgcm with MPI support are: |
| 714 |
\begin{enumerate} |
| 715 |
|
| 716 |
\item Determine the locations of your MPI-enabled compiler and/or MPI |
| 717 |
libraries and put them into an options file as described in Section |
| 718 |
\ref{sect:genmake}. One can start with one of the examples in: |
| 719 |
\begin{rawhtml} <A |
| 720 |
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/"> |
| 721 |
\end{rawhtml} |
| 722 |
\begin{center} |
| 723 |
\texttt{MITgcm/tools/build\_options/} |
| 724 |
\end{center} |
| 725 |
\begin{rawhtml} </A> \end{rawhtml} |
| 726 |
such as \texttt{linux\_ia32\_g77+mpi\_cg01} or |
| 727 |
\texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at |
| 728 |
hand. You may need help from your user guide or local systems |
| 729 |
administrator to determine the exact location of the MPI libraries. |
| 730 |
If libraries are not installed, MPI implementations and related |
| 731 |
tools are available including: |
| 732 |
\begin{itemize} |
| 733 |
\item \begin{rawhtml} <A |
| 734 |
href="http://www-unix.mcs.anl.gov/mpi/mpich/"> |
| 735 |
\end{rawhtml} |
| 736 |
MPICH |
| 737 |
\begin{rawhtml} </A> \end{rawhtml} |
| 738 |
|
| 739 |
\item \begin{rawhtml} <A |
| 740 |
href="http://www.lam-mpi.org/"> |
| 741 |
\end{rawhtml} |
| 742 |
LAM/MPI |
| 743 |
\begin{rawhtml} </A> \end{rawhtml} |
| 744 |
|
| 745 |
\item \begin{rawhtml} <A |
| 746 |
href="http://www.osc.edu/~pw/mpiexec/"> |
| 747 |
\end{rawhtml} |
| 748 |
MPIexec |
| 749 |
\begin{rawhtml} </A> \end{rawhtml} |
| 750 |
\end{itemize} |
| 751 |
|
| 752 |
\item Build the code with the \texttt{genmake2} \texttt{-mpi} option |
| 753 |
(see Section \ref{sect:genmake}) using commands such as: |
| 754 |
{\footnotesize \begin{verbatim} |
| 755 |
% ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE |
| 756 |
% make depend |
| 757 |
% make |
| 758 |
\end{verbatim} } |
| 759 |
|
| 760 |
\item Run the code with the appropriate MPI ``run'' or ``exec'' |
| 761 |
program provided with your particular implementation of MPI. |
| 762 |
Typical MPI packages such as MPICH will use something like: |
| 763 |
\begin{verbatim} |
| 764 |
% mpirun -np 4 -machinefile mf ./mitgcmuv |
| 765 |
\end{verbatim} |
| 766 |
Sightly more complicated scripts may be needed for many machines |
| 767 |
since execution of the code may be controlled by both the MPI |
| 768 |
library and a job scheduling and queueing system such as PBS, |
| 769 |
LoadLeveller, Condor, or any of a number of similar tools. A few |
| 770 |
example scripts (those used for our \begin{rawhtml} <A |
| 771 |
href="http://mitgcm.org/testing.html"> \end{rawhtml}regular |
| 772 |
verification runs\begin{rawhtml} </A> \end{rawhtml}) are available |
| 773 |
at: |
| 774 |
\begin{rawhtml} <A |
| 775 |
href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/"> |
| 776 |
\end{rawhtml} |
| 777 |
{\footnotesize \tt |
| 778 |
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ } |
| 779 |
\begin{rawhtml} </A> \end{rawhtml} |
| 780 |
|
| 781 |
\end{enumerate} |
| 782 |
|
| 783 |
An example of the above process on the MITgcm cluster (``cg01'') using |
| 784 |
the GNU g77 compiler and the mpich MPI library is: |
| 785 |
|
| 786 |
{\footnotesize \begin{verbatim} |
| 787 |
% cd MITgcm/verification/exp5 |
| 788 |
% mkdir build |
| 789 |
% cd build |
| 790 |
% ../../../tools/genmake2 -mpi -mods=../code \ |
| 791 |
-of=../../../tools/build_options/linux_ia32_g77+mpi_cg01 |
| 792 |
% make depend |
| 793 |
% make |
| 794 |
% cd ../input |
| 795 |
% /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \ |
| 796 |
-machinefile mf --gm-kill 5 -v -np 2 ../build/mitgcmuv |
| 797 |
\end{verbatim} } |
| 798 |
|
| 799 |
\section[Running MITgcm]{Running the model in prognostic mode} |
| 800 |
\label{sect:runModel} |
| 801 |
\begin{rawhtml} |
| 802 |
<!-- CMIREDIR:runModel: --> |
| 803 |
\end{rawhtml} |
| 804 |
|
| 805 |
If compilation finished succesfully (section \ref{sect:buildingCode}) |
| 806 |
then an executable called \texttt{mitgcmuv} will now exist in the |
| 807 |
local directory. |
| 808 |
|
| 809 |
To run the model as a single process (\textit{ie.} not in parallel) |
| 810 |
simply type: |
| 811 |
\begin{verbatim} |
| 812 |
% ./mitgcmuv |
| 813 |
\end{verbatim} |
| 814 |
The ``./'' is a safe-guard to make sure you use the local executable |
| 815 |
in case you have others that exist in your path (surely odd if you |
| 816 |
do!). The above command will spew out many lines of text output to |
| 817 |
your screen. This output contains details such as parameter values as |
| 818 |
well as diagnostics such as mean Kinetic energy, largest CFL number, |
| 819 |
etc. It is worth keeping this text output with the binary output so we |
| 820 |
normally re-direct the \texttt{stdout} stream as follows: |
| 821 |
\begin{verbatim} |
| 822 |
% ./mitgcmuv > output.txt |
| 823 |
\end{verbatim} |
| 824 |
In the event that the model encounters an error and stops, it is very |
| 825 |
helpful to include the last few line of this \texttt{output.txt} file |
| 826 |
along with the (\texttt{stderr}) error message within any bug reports. |
| 827 |
|
| 828 |
For the example experiments in \texttt{verification}, an example of the |
| 829 |
output is kept in \texttt{results/output.txt} for comparison. You can |
| 830 |
compare your \texttt{output.txt} with the corresponding one for that |
| 831 |
experiment to check that the set-up works. |
| 832 |
|
| 833 |
|
| 834 |
|
| 835 |
\subsection{Output files} |
| 836 |
|
| 837 |
The model produces various output files and, when using \texttt{mnc}, |
| 838 |
sometimes even directories. Depending upon the I/O package(s) |
| 839 |
selected at compile time (either \texttt{mdsio} or \texttt{mnc} or |
| 840 |
both as determined by \texttt{code/packages.conf}) and the run-time |
| 841 |
flags set (in \texttt{input/data.pkg}), the following output may |
| 842 |
appear. |
| 843 |
|
| 844 |
|
| 845 |
\subsubsection{MDSIO output files} |
| 846 |
|
| 847 |
The ``traditional'' output files are generated by the \texttt{mdsio} |
| 848 |
package. At a minimum, the instantaneous ``state'' of the model is |
| 849 |
written out, which is made of the following files: |
| 850 |
|
| 851 |
\begin{itemize} |
| 852 |
\item \texttt{U.00000nIter} - zonal component of velocity field (m/s |
| 853 |
and positive eastward). |
| 854 |
|
| 855 |
\item \texttt{V.00000nIter} - meridional component of velocity field |
| 856 |
(m/s and positive northward). |
| 857 |
|
| 858 |
\item \texttt{W.00000nIter} - vertical component of velocity field |
| 859 |
(ocean: m/s and positive upward, atmosphere: Pa/s and positive |
| 860 |
towards increasing pressure i.e. downward). |
| 861 |
|
| 862 |
\item \texttt{T.00000nIter} - potential temperature (ocean: |
| 863 |
$^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$). |
| 864 |
|
| 865 |
\item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water |
| 866 |
vapor (g/kg). |
| 867 |
|
| 868 |
\item \texttt{Eta.00000nIter} - ocean: surface elevation (m), |
| 869 |
atmosphere: surface pressure anomaly (Pa). |
| 870 |
\end{itemize} |
| 871 |
|
| 872 |
The chain \texttt{00000nIter} consists of ten figures that specify the |
| 873 |
iteration number at which the output is written out. For example, |
| 874 |
\texttt{U.0000000300} is the zonal velocity at iteration 300. |
| 875 |
|
| 876 |
In addition, a ``pickup'' or ``checkpoint'' file called: |
| 877 |
|
| 878 |
\begin{itemize} |
| 879 |
\item \texttt{pickup.00000nIter} |
| 880 |
\end{itemize} |
| 881 |
|
| 882 |
is written out. This file represents the state of the model in a condensed |
| 883 |
form and is used for restarting the integration. If the C-D scheme is used, |
| 884 |
there is an additional ``pickup'' file: |
| 885 |
|
| 886 |
\begin{itemize} |
| 887 |
\item \texttt{pickup\_cd.00000nIter} |
| 888 |
\end{itemize} |
| 889 |
|
| 890 |
containing the D-grid velocity data and that has to be written out as well |
| 891 |
in order to restart the integration. Rolling checkpoint files are the same |
| 892 |
as the pickup files but are named differently. Their name contain the chain |
| 893 |
\texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be |
| 894 |
used to restart the model but are overwritten every other time they are |
| 895 |
output to save disk space during long integrations. |
| 896 |
|
| 897 |
|
| 898 |
|
| 899 |
\subsubsection{MNC output files} |
| 900 |
|
| 901 |
Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output |
| 902 |
is usually (though not necessarily) placed within a subdirectory with |
| 903 |
a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}. The files |
| 904 |
within this subdirectory are all in the ``self-describing'' netCDF |
| 905 |
format and can thus be browsed and/or plotted using tools such as: |
| 906 |
\begin{itemize} |
| 907 |
\item \texttt{ncdump} is a utility which is typically included |
| 908 |
with every netCDF install: |
| 909 |
\begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml} |
| 910 |
\begin{verbatim} |
| 911 |
http://www.unidata.ucar.edu/packages/netcdf/ |
| 912 |
\end{verbatim} |
| 913 |
\begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF |
| 914 |
binaries into formatted ASCII text files. |
| 915 |
|
| 916 |
\item \texttt{ncview} utility is a very convenient and quick way |
| 917 |
to plot netCDF data and it runs on most OSes: |
| 918 |
\begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml} |
| 919 |
\begin{verbatim} |
| 920 |
http://meteora.ucsd.edu/~pierce/ncview_home_page.html |
| 921 |
\end{verbatim} |
| 922 |
\begin{rawhtml} </A> \end{rawhtml} |
| 923 |
|
| 924 |
\item MatLAB(c) and other common post-processing environments provide |
| 925 |
various netCDF interfaces including: |
| 926 |
\begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml} |
| 927 |
\begin{verbatim} |
| 928 |
http://mexcdf.sourceforge.net/ |
| 929 |
\end{verbatim} |
| 930 |
\begin{rawhtml} </A> \end{rawhtml} |
| 931 |
\begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml} |
| 932 |
\begin{verbatim} |
| 933 |
http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html |
| 934 |
\end{verbatim} |
| 935 |
\begin{rawhtml} </A> \end{rawhtml} |
| 936 |
\end{itemize} |
| 937 |
|
| 938 |
|
| 939 |
\subsection{Looking at the output} |
| 940 |
|
| 941 |
The ``traditional'' or mdsio model data are written according to a |
| 942 |
``meta/data'' file format. Each variable is associated with two files |
| 943 |
with suffix names \texttt{.data} and \texttt{.meta}. The |
| 944 |
\texttt{.data} file contains the data written in binary form |
| 945 |
(big\_endian by default). The \texttt{.meta} file is a ``header'' file |
| 946 |
that contains information about the size and the structure of the |
| 947 |
\texttt{.data} file. This way of organizing the output is particularly |
| 948 |
useful when running multi-processors calculations. The base version of |
| 949 |
the model includes a few matlab utilities to read output files written |
| 950 |
in this format. The matlab scripts are located in the directory |
| 951 |
\texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m} |
| 952 |
reads the data. Look at the comments inside the script to see how to |
| 953 |
use it. |
| 954 |
|
| 955 |
Some examples of reading and visualizing some output in {\em Matlab}: |
| 956 |
\begin{verbatim} |
| 957 |
% matlab |
| 958 |
>> H=rdmds('Depth'); |
| 959 |
>> contourf(H');colorbar; |
| 960 |
>> title('Depth of fluid as used by model'); |
| 961 |
|
| 962 |
>> eta=rdmds('Eta',10); |
| 963 |
>> imagesc(eta');axis ij;colorbar; |
| 964 |
>> title('Surface height at iter=10'); |
| 965 |
|
| 966 |
>> eta=rdmds('Eta',[0:10:100]); |
| 967 |
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end |
| 968 |
\end{verbatim} |
| 969 |
|
| 970 |
Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and |
| 971 |
they are described in Section \ref{sec:pkg:mnc}. |
| 972 |
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