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% $Header: /u/gcmpack/manual/part3/getting_started.tex,v 1.33 2006/04/08 01:50:49 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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|
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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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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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\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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|
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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} |
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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: |
| 209 |
\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 |
| 254 |
patch then you'll need to get the latest code: |
| 255 |
\begin{verbatim} |
| 256 |
% cvs -q update -A -d -P |
| 257 |
\end{verbatim} |
| 258 |
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 |
| 260 |
very latest version. As a rule, we don't recommend this since you |
| 261 |
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 |
| 263 |
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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\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 |
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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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\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 |
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\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{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 \texttt{diags}: contains the code relative to time-averaged |
| 294 |
diagnostics. It is subdivided into two subdirectories \texttt{inc} |
| 295 |
and \texttt{src} that contain include files (\texttt{*.h} files) and |
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Fortran subroutines (\texttt{*.F} files), respectively. |
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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. |
| 301 |
Also subdivided into two subdirectories \texttt{inc} and |
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\texttt{src}. |
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|
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\item \texttt{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 \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} |
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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 section 3. |
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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) |
| 319 |
that should be used to generate your makefile. The directory |
| 320 |
\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 details in part V. |
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|
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\item \texttt{utils}: this directory contains various utilities. The |
| 325 |
subdirectory \texttt{knudsen2} contains code and a makefile that |
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compute coefficients of the polynomial approximation to the knudsen |
| 327 |
formula for an ocean nonlinear equation of state. The |
| 328 |
\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. |
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|
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\item \texttt{verification}: this directory contains the model |
| 334 |
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[MITgcm Example Experiments]{Example experiments} |
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\label{sect:modelExamples} |
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\begin{rawhtml} |
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<!-- CMIREDIR:modelExamples: --> |
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\end{rawhtml} |
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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 full MITgcm distribution comes with more than a dozen |
| 347 |
pre-configured numerical experiments. Some of these example |
| 348 |
experiments are tests of individual parts of the model code, but many |
| 349 |
are fully fledged numerical simulations. A few of the examples are |
| 350 |
used for tutorial documentation in sections \ref{sect:eg-baro} - |
| 351 |
\ref{sect:eg-global}. The other examples follow the same general |
| 352 |
structure as the tutorial examples. However, they only include brief |
| 353 |
instructions in a text file called {\it README}. The examples are |
| 354 |
located in subdirectories under the directory \texttt{verification}. |
| 355 |
Each example is briefly described below. |
| 356 |
|
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\subsection{Full list of model examples} |
| 358 |
|
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\begin{enumerate} |
| 360 |
|
| 361 |
\item \texttt{exp0} - single layer, ocean double gyre (barotropic with |
| 362 |
free-surface). This experiment is described in detail in section |
| 363 |
\ref{sect:eg-baro}. |
| 364 |
|
| 365 |
\item \texttt{exp1} - Four layer, ocean double gyre. This experiment |
| 366 |
is described in detail in section \ref{sect:eg-baroc}. |
| 367 |
|
| 368 |
\item \texttt{exp2} - 4x4 degree global ocean simulation with steady |
| 369 |
climatological forcing. This experiment is described in detail in |
| 370 |
section \ref{sect:eg-global}. |
| 371 |
|
| 372 |
\item \texttt{exp4} - Flow over a Gaussian bump in open-water or |
| 373 |
channel with open boundaries. |
| 374 |
|
| 375 |
\item \texttt{exp5} - Inhomogenously forced ocean convection in a |
| 376 |
doubly periodic box. |
| 377 |
|
| 378 |
\item \texttt{front\_relax} - Relaxation of an ocean thermal front (test for |
| 379 |
Gent/McWilliams scheme). 2D (Y-Z). |
| 380 |
|
| 381 |
\item \texttt{internal wave} - Ocean internal wave forced by open |
| 382 |
boundary conditions. |
| 383 |
|
| 384 |
\item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP |
| 385 |
scheme; 1 month integration |
| 386 |
|
| 387 |
\item \texttt{hs94.1x64x5} - Zonal averaged atmosphere using Held and |
| 388 |
Suarez '94 forcing. |
| 389 |
|
| 390 |
\item \texttt{hs94.128x64x5} - 3D atmosphere dynamics using Held and |
| 391 |
Suarez '94 forcing. |
| 392 |
|
| 393 |
\item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and |
| 394 |
Suarez '94 forcing on the cubed sphere. |
| 395 |
|
| 396 |
\item \texttt{aim.5l\_zon-ave} - Intermediate Atmospheric physics. |
| 397 |
Global Zonal Mean configuration, 1x64x5 resolution. |
| 398 |
|
| 399 |
\item \texttt{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate |
| 400 |
Atmospheric physics, equatorial Slice configuration. 2D (X-Z). |
| 401 |
|
| 402 |
\item \texttt{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric |
| 403 |
physics. 3D Equatorial Channel configuration. |
| 404 |
|
| 405 |
\item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics. |
| 406 |
Global configuration, on latitude longitude grid with 128x64x5 grid |
| 407 |
points ($2.8^\circ$ resolution). |
| 408 |
|
| 409 |
\item \texttt{adjustment.128x64x1} Barotropic adjustment problem on |
| 410 |
latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution). |
| 411 |
|
| 412 |
\item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on |
| 413 |
cube sphere grid with 32x32 points per face (roughly $2.8^\circ$ |
| 414 |
resolution). |
| 415 |
|
| 416 |
\item \texttt{advect\_cs} Two-dimensional passive advection test on |
| 417 |
cube sphere grid. |
| 418 |
|
| 419 |
\item \texttt{advect\_xy} Two-dimensional (horizontal plane) passive |
| 420 |
advection test on Cartesian grid. |
| 421 |
|
| 422 |
\item \texttt{advect\_yz} Two-dimensional (vertical plane) passive |
| 423 |
advection test on Cartesian grid. |
| 424 |
|
| 425 |
\item \texttt{carbon} Simple passive tracer experiment. Includes |
| 426 |
derivative calculation. Described in detail in section |
| 427 |
\ref{sect:eg-carbon-ad}. |
| 428 |
|
| 429 |
\item \texttt{flt\_example} Example of using float package. |
| 430 |
|
| 431 |
\item \texttt{global\_ocean.90x40x15} Global circulation with GM, flux |
| 432 |
boundary conditions and poles. |
| 433 |
|
| 434 |
\item \texttt{global\_ocean\_pressure} Global circulation in pressure |
| 435 |
coordinate (non-Boussinesq ocean model). Described in detail in |
| 436 |
section \ref{sect:eg-globalpressure}. |
| 437 |
|
| 438 |
\item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube |
| 439 |
sphere grid. |
| 440 |
|
| 441 |
\end{enumerate} |
| 442 |
|
| 443 |
\subsection{Directory structure of model examples} |
| 444 |
|
| 445 |
Each example directory has the following subdirectories: |
| 446 |
|
| 447 |
\begin{itemize} |
| 448 |
\item \texttt{code}: contains the code particular to the example. At a |
| 449 |
minimum, this directory includes the following files: |
| 450 |
|
| 451 |
\begin{itemize} |
| 452 |
\item \texttt{code/packages.conf}: declares the list of packages or |
| 453 |
package groups to be used. If not included, the default version |
| 454 |
is located in \texttt{pkg/pkg\_default}. Package groups are |
| 455 |
simply convenient collections of commonly used packages which are |
| 456 |
defined in \texttt{pkg/pkg\_default}. Some packages may require |
| 457 |
other packages or may require their absence (that is, they are |
| 458 |
incompatible) and these package dependencies are listed in |
| 459 |
\texttt{pkg/pkg\_depend}. |
| 460 |
|
| 461 |
\item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to |
| 462 |
the ``execution environment'' part of the code. The default |
| 463 |
version is located in \texttt{eesupp/inc}. |
| 464 |
|
| 465 |
\item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to |
| 466 |
the ``numerical model'' part of the code. The default version is |
| 467 |
located in \texttt{model/inc}. |
| 468 |
|
| 469 |
\item \texttt{code/SIZE.h}: declares size of underlying |
| 470 |
computational grid. The default version is located in |
| 471 |
\texttt{model/inc}. |
| 472 |
\end{itemize} |
| 473 |
|
| 474 |
In addition, other include files and subroutines might be present in |
| 475 |
\texttt{code} depending on the particular experiment. See Section 2 |
| 476 |
for more details. |
| 477 |
|
| 478 |
\item \texttt{input}: contains the input data files required to run |
| 479 |
the example. At a minimum, the \texttt{input} directory contains the |
| 480 |
following files: |
| 481 |
|
| 482 |
\begin{itemize} |
| 483 |
\item \texttt{input/data}: this file, written as a namelist, |
| 484 |
specifies the main parameters for the experiment. |
| 485 |
|
| 486 |
\item \texttt{input/data.pkg}: contains parameters relative to the |
| 487 |
packages used in the experiment. |
| 488 |
|
| 489 |
\item \texttt{input/eedata}: this file contains ``execution |
| 490 |
environment'' data. At present, this consists of a specification |
| 491 |
of the number of threads to use in $X$ and $Y$ under multithreaded |
| 492 |
execution. |
| 493 |
\end{itemize} |
| 494 |
|
| 495 |
In addition, you will also find in this directory the forcing and |
| 496 |
topography files as well as the files describing the initial state |
| 497 |
of the experiment. This varies from experiment to experiment. See |
| 498 |
section 2 for more details. |
| 499 |
|
| 500 |
\item \texttt{results}: this directory contains the output file |
| 501 |
\texttt{output.txt} produced by the simulation example. This file is |
| 502 |
useful for comparison with your own output when you run the |
| 503 |
experiment. |
| 504 |
\end{itemize} |
| 505 |
|
| 506 |
Once you have chosen the example you want to run, you are ready to |
| 507 |
compile the code. |
| 508 |
|
| 509 |
\section[Building MITgcm]{Building the code} |
| 510 |
\label{sect:buildingCode} |
| 511 |
\begin{rawhtml} |
| 512 |
<!-- CMIREDIR:buildingCode: --> |
| 513 |
\end{rawhtml} |
| 514 |
|
| 515 |
To compile the code, we use the \texttt{make} program. This uses a |
| 516 |
file (\texttt{Makefile}) that allows us to pre-process source files, |
| 517 |
specify compiler and optimization options and also figures out any |
| 518 |
file dependencies. We supply a script (\texttt{genmake2}), described |
| 519 |
in section \ref{sect:genmake}, that automatically creates the |
| 520 |
\texttt{Makefile} for you. You then need to build the dependencies and |
| 521 |
compile the code. |
| 522 |
|
| 523 |
As an example, assume that you want to build and run experiment |
| 524 |
\texttt{verification/exp2}. The are multiple ways and places to |
| 525 |
actually do this but here let's build the code in |
| 526 |
\texttt{verification/exp2/build}: |
| 527 |
\begin{verbatim} |
| 528 |
% cd verification/exp2/build |
| 529 |
\end{verbatim} |
| 530 |
First, build the \texttt{Makefile}: |
| 531 |
\begin{verbatim} |
| 532 |
% ../../../tools/genmake2 -mods=../code |
| 533 |
\end{verbatim} |
| 534 |
The command line option tells \texttt{genmake} to override model source |
| 535 |
code with any files in the directory \texttt{../code/}. |
| 536 |
|
| 537 |
On many systems, the \texttt{genmake2} program will be able to |
| 538 |
automatically recognize the hardware, find compilers and other tools |
| 539 |
within the user's path (``\texttt{echo \$PATH}''), and then choose an |
| 540 |
appropriate set of options from the files (``optfiles'') contained in |
| 541 |
the \texttt{tools/build\_options} directory. Under some |
| 542 |
circumstances, a user may have to create a new ``optfile'' in order to |
| 543 |
specify the exact combination of compiler, compiler flags, libraries, |
| 544 |
and other options necessary to build a particular configuration of |
| 545 |
MITgcm. In such cases, it is generally helpful to read the existing |
| 546 |
``optfiles'' and mimic their syntax. |
| 547 |
|
| 548 |
Through the MITgcm-support list, the MITgcm developers are willing to |
| 549 |
provide help writing or modifing ``optfiles''. And we encourage users |
| 550 |
to post new ``optfiles'' (particularly ones for new machines or |
| 551 |
architectures) to the |
| 552 |
\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml} |
| 553 |
MITgcm-support@mitgcm.org |
| 554 |
\begin{rawhtml} </A> \end{rawhtml} |
| 555 |
list. |
| 556 |
|
| 557 |
To specify an optfile to \texttt{genmake2}, the syntax is: |
| 558 |
\begin{verbatim} |
| 559 |
% ../../../tools/genmake2 -mods=../code -of /path/to/optfile |
| 560 |
\end{verbatim} |
| 561 |
|
| 562 |
Once a \texttt{Makefile} has been generated, we create the |
| 563 |
dependencies with the command: |
| 564 |
\begin{verbatim} |
| 565 |
% make depend |
| 566 |
\end{verbatim} |
| 567 |
This modifies the \texttt{Makefile} by attaching a (usually, long) |
| 568 |
list of files upon which other files depend. The purpose of this is to |
| 569 |
reduce re-compilation if and when you start to modify the code. The |
| 570 |
{\tt make depend} command also creates links from the model source to |
| 571 |
this directory. It is important to note that the {\tt make depend} |
| 572 |
stage will occasionally produce warnings or errors since the |
| 573 |
dependency parsing tool is unable to find all of the necessary header |
| 574 |
files (\textit{eg.} \texttt{netcdf.inc}). In these circumstances, it |
| 575 |
is usually OK to ignore the warnings/errors and proceed to the next |
| 576 |
step. |
| 577 |
|
| 578 |
Next one can compile the code using: |
| 579 |
\begin{verbatim} |
| 580 |
% make |
| 581 |
\end{verbatim} |
| 582 |
The {\tt make} command creates an executable called \texttt{mitgcmuv}. |
| 583 |
Additional make ``targets'' are defined within the makefile to aid in |
| 584 |
the production of adjoint and other versions of MITgcm. On SMP |
| 585 |
(shared multi-processor) systems, the build process can often be sped |
| 586 |
up appreciably using the command: |
| 587 |
\begin{verbatim} |
| 588 |
% make -j 2 |
| 589 |
\end{verbatim} |
| 590 |
where the ``2'' can be replaced with a number that corresponds to the |
| 591 |
number of CPUs available. |
| 592 |
|
| 593 |
Now you are ready to run the model. General instructions for doing so are |
| 594 |
given in section \ref{sect:runModel}. Here, we can run the model by |
| 595 |
first creating links to all the input files: |
| 596 |
\begin{verbatim} |
| 597 |
ln -s ../input/* . |
| 598 |
\end{verbatim} |
| 599 |
and then calling the executable with: |
| 600 |
\begin{verbatim} |
| 601 |
./mitgcmuv > output.txt |
| 602 |
\end{verbatim} |
| 603 |
where we are re-directing the stream of text output to the file |
| 604 |
\texttt{output.txt}. |
| 605 |
|
| 606 |
|
| 607 |
\section[Running MITgcm]{Running the model in prognostic mode} |
| 608 |
\label{sect:runModel} |
| 609 |
\begin{rawhtml} |
| 610 |
<!-- CMIREDIR:runModel: --> |
| 611 |
\end{rawhtml} |
| 612 |
|
| 613 |
If compilation finished succesfully (section \ref{sect:buildingCode}) |
| 614 |
then an executable called \texttt{mitgcmuv} will now exist in the |
| 615 |
local directory. |
| 616 |
|
| 617 |
To run the model as a single process (\textit{ie.} not in parallel) |
| 618 |
simply type: |
| 619 |
\begin{verbatim} |
| 620 |
% ./mitgcmuv |
| 621 |
\end{verbatim} |
| 622 |
The ``./'' is a safe-guard to make sure you use the local executable |
| 623 |
in case you have others that exist in your path (surely odd if you |
| 624 |
do!). The above command will spew out many lines of text output to |
| 625 |
your screen. This output contains details such as parameter values as |
| 626 |
well as diagnostics such as mean Kinetic energy, largest CFL number, |
| 627 |
etc. It is worth keeping this text output with the binary output so we |
| 628 |
normally re-direct the \texttt{stdout} stream as follows: |
| 629 |
\begin{verbatim} |
| 630 |
% ./mitgcmuv > output.txt |
| 631 |
\end{verbatim} |
| 632 |
In the event that the model encounters an error and stops, it is very |
| 633 |
helpful to include the last few line of this \texttt{output.txt} file |
| 634 |
along with the (\texttt{stderr}) error message within any bug reports. |
| 635 |
|
| 636 |
For the example experiments in \texttt{verification}, an example of the |
| 637 |
output is kept in \texttt{results/output.txt} for comparison. You can |
| 638 |
compare your \texttt{output.txt} with the corresponding one for that |
| 639 |
experiment to check that the set-up works. |
| 640 |
|
| 641 |
|
| 642 |
|
| 643 |
\subsection{Output files} |
| 644 |
|
| 645 |
The model produces various output files and, when using \texttt{mnc}, |
| 646 |
sometimes even directories. Depending upon the I/O package(s) |
| 647 |
selected at compile time (either \texttt{mdsio} or \texttt{mnc} or |
| 648 |
both as determined by \texttt{code/packages.conf}) and the run-time |
| 649 |
flags set (in \texttt{input/data.pkg}), the following output may |
| 650 |
appear. |
| 651 |
|
| 652 |
|
| 653 |
\subsubsection{MDSIO output files} |
| 654 |
|
| 655 |
The ``traditional'' output files are generated by the \texttt{mdsio} |
| 656 |
package. At a minimum, the instantaneous ``state'' of the model is |
| 657 |
written out, which is made of the following files: |
| 658 |
|
| 659 |
\begin{itemize} |
| 660 |
\item \texttt{U.00000nIter} - zonal component of velocity field (m/s |
| 661 |
and positive eastward). |
| 662 |
|
| 663 |
\item \texttt{V.00000nIter} - meridional component of velocity field |
| 664 |
(m/s and positive northward). |
| 665 |
|
| 666 |
\item \texttt{W.00000nIter} - vertical component of velocity field |
| 667 |
(ocean: m/s and positive upward, atmosphere: Pa/s and positive |
| 668 |
towards increasing pressure i.e. downward). |
| 669 |
|
| 670 |
\item \texttt{T.00000nIter} - potential temperature (ocean: |
| 671 |
$^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$). |
| 672 |
|
| 673 |
\item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water |
| 674 |
vapor (g/kg). |
| 675 |
|
| 676 |
\item \texttt{Eta.00000nIter} - ocean: surface elevation (m), |
| 677 |
atmosphere: surface pressure anomaly (Pa). |
| 678 |
\end{itemize} |
| 679 |
|
| 680 |
The chain \texttt{00000nIter} consists of ten figures that specify the |
| 681 |
iteration number at which the output is written out. For example, |
| 682 |
\texttt{U.0000000300} is the zonal velocity at iteration 300. |
| 683 |
|
| 684 |
In addition, a ``pickup'' or ``checkpoint'' file called: |
| 685 |
|
| 686 |
\begin{itemize} |
| 687 |
\item \texttt{pickup.00000nIter} |
| 688 |
\end{itemize} |
| 689 |
|
| 690 |
is written out. This file represents the state of the model in a condensed |
| 691 |
form and is used for restarting the integration. If the C-D scheme is used, |
| 692 |
there is an additional ``pickup'' file: |
| 693 |
|
| 694 |
\begin{itemize} |
| 695 |
\item \texttt{pickup\_cd.00000nIter} |
| 696 |
\end{itemize} |
| 697 |
|
| 698 |
containing the D-grid velocity data and that has to be written out as well |
| 699 |
in order to restart the integration. Rolling checkpoint files are the same |
| 700 |
as the pickup files but are named differently. Their name contain the chain |
| 701 |
\texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be |
| 702 |
used to restart the model but are overwritten every other time they are |
| 703 |
output to save disk space during long integrations. |
| 704 |
|
| 705 |
|
| 706 |
|
| 707 |
\subsubsection{MNC output files} |
| 708 |
|
| 709 |
Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output |
| 710 |
is usually (though not necessarily) placed within a subdirectory with |
| 711 |
a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}. The files |
| 712 |
within this subdirectory are all in the ``self-describing'' netCDF |
| 713 |
format and can thus be browsed and/or plotted using tools such as: |
| 714 |
\begin{itemize} |
| 715 |
\item \texttt{ncdump} is a utility which is typically included |
| 716 |
with every netCDF install: |
| 717 |
\begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml} |
| 718 |
\begin{verbatim} |
| 719 |
http://www.unidata.ucar.edu/packages/netcdf/ |
| 720 |
\end{verbatim} |
| 721 |
\begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF |
| 722 |
binaries into formatted ASCII text files. |
| 723 |
|
| 724 |
\item \texttt{ncview} utility is a very convenient and quick way |
| 725 |
to plot netCDF data and it runs on most OSes: |
| 726 |
\begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml} |
| 727 |
\begin{verbatim} |
| 728 |
http://meteora.ucsd.edu/~pierce/ncview_home_page.html |
| 729 |
\end{verbatim} |
| 730 |
\begin{rawhtml} </A> \end{rawhtml} |
| 731 |
|
| 732 |
\item MatLAB(c) and other common post-processing environments provide |
| 733 |
various netCDF interfaces including: |
| 734 |
\begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml} |
| 735 |
\begin{verbatim} |
| 736 |
http://mexcdf.sourceforge.net/ |
| 737 |
\end{verbatim} |
| 738 |
\begin{rawhtml} </A> \end{rawhtml} |
| 739 |
\begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml} |
| 740 |
\begin{verbatim} |
| 741 |
http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html |
| 742 |
\end{verbatim} |
| 743 |
\begin{rawhtml} </A> \end{rawhtml} |
| 744 |
\end{itemize} |
| 745 |
|
| 746 |
|
| 747 |
\subsection{Looking at the output} |
| 748 |
|
| 749 |
The ``traditional'' or mdsio model data are written according to a |
| 750 |
``meta/data'' file format. Each variable is associated with two files |
| 751 |
with suffix names \texttt{.data} and \texttt{.meta}. The |
| 752 |
\texttt{.data} file contains the data written in binary form |
| 753 |
(big\_endian by default). The \texttt{.meta} file is a ``header'' file |
| 754 |
that contains information about the size and the structure of the |
| 755 |
\texttt{.data} file. This way of organizing the output is particularly |
| 756 |
useful when running multi-processors calculations. The base version of |
| 757 |
the model includes a few matlab utilities to read output files written |
| 758 |
in this format. The matlab scripts are located in the directory |
| 759 |
\texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m} |
| 760 |
reads the data. Look at the comments inside the script to see how to |
| 761 |
use it. |
| 762 |
|
| 763 |
Some examples of reading and visualizing some output in {\em Matlab}: |
| 764 |
\begin{verbatim} |
| 765 |
% matlab |
| 766 |
>> H=rdmds('Depth'); |
| 767 |
>> contourf(H');colorbar; |
| 768 |
>> title('Depth of fluid as used by model'); |
| 769 |
|
| 770 |
>> eta=rdmds('Eta',10); |
| 771 |
>> imagesc(eta');axis ij;colorbar; |
| 772 |
>> title('Surface height at iter=10'); |
| 773 |
|
| 774 |
>> eta=rdmds('Eta',[0:10:100]); |
| 775 |
>> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end |
| 776 |
\end{verbatim} |
| 777 |
|
| 778 |
Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and |
| 779 |
they are described in Section \ref{sec:pkg:mnc}. |
| 780 |
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