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revision 1.42 by jmc, Fri May 28 02:09:59 2010 UTC revision 1.45 by jmc, Wed May 11 18:58:02 2011 UTC
# Line 14  are described more fully in chapters \re Line 14  are described more fully in chapters \re
14  \ref{chap:sarch}.  \ref{chap:sarch}.
15    
16  \section{Where to find information}  \section{Where to find information}
17  \label{sect:whereToFindInfo}  \label{sec:whereToFindInfo}
18  \begin{rawhtml}  \begin{rawhtml}
19  <!-- CMIREDIR:whereToFindInfo: -->  <!-- CMIREDIR:whereToFindInfo: -->
20  \end{rawhtml}  \end{rawhtml}
# Line 29  http://mitgcm.org/pipermail/mitgcm-suppo Line 29  http://mitgcm.org/pipermail/mitgcm-suppo
29  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
30    
31  \section{Obtaining the code}  \section{Obtaining the code}
32  \label{sect:obtainingCode}  \label{sec:obtainingCode}
33  \begin{rawhtml}  \begin{rawhtml}
34  <!-- CMIREDIR:obtainingCode: -->  <!-- CMIREDIR:obtainingCode: -->
35  \end{rawhtml}  \end{rawhtml}
# Line 63  provide easy support for maintenance upd Line 63  provide easy support for maintenance upd
63  \end{enumerate}  \end{enumerate}
64    
65  \subsection{Method 1 - Checkout from CVS}  \subsection{Method 1 - Checkout from CVS}
66  \label{sect:cvs_checkout}  \label{sec:cvs_checkout}
67    
68  If CVS is available on your system, we strongly encourage you to use it. CVS  If CVS is available on your system, we strongly encourage you to use it. CVS
69  provides an efficient and elegant way of organizing your code and keeping  provides an efficient and elegant way of organizing your code and keeping
# Line 92  You only need to do a ``cvs login'' once Line 92  You only need to do a ``cvs login'' once
92    
93  To obtain the latest sources type:  To obtain the latest sources type:
94  \begin{verbatim}  \begin{verbatim}
95  % cvs co MITgcm  % cvs co -P MITgcm
96  \end{verbatim}  \end{verbatim}
97  or to get a specific release type:  or to get a specific release type:
98  \begin{verbatim}  \begin{verbatim}
99  % cvs co -P -r checkpoint52i_post  MITgcm  % cvs co -P -r checkpoint52i_post MITgcm
100  \end{verbatim}  \end{verbatim}
101    The CVS command ``\texttt{cvs co}'' is the abreviation of the full-name
102    ``\texttt{cvs checkout}'' command and using the option ``-P'' (\texttt{cvs co -P})
103    will prevent to download unnecessary empty directories.
104    
105  The MITgcm web site contains further directions concerning the source  The MITgcm web site contains further directions concerning the source
106  code and CVS.  It also contains a web interface to our CVS archive so  code and CVS.  It also contains a web interface to our CVS archive so
107  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
108  development milestones:  development milestones:
 %\begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}  
109  \begin{rawhtml} <A href="http://mitgcm.org/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
110  \begin{verbatim}  \begin{verbatim}
111  http://mitgcm.org/source_code.html  http://mitgcm.org/viewvc/MITgcm/MITgcm/
112  \end{verbatim}  \end{verbatim}
113  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
114    
# Line 149  It is important to note that the CVS ali Line 152  It is important to note that the CVS ali
152  \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories  \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
153  they create can be changed to a different name following the check-out:  they create can be changed to a different name following the check-out:
154  \begin{verbatim}  \begin{verbatim}
155     %  cvs co MITgcm_verif_basic     %  cvs co -P MITgcm_verif_basic
156     %  mv MITgcm MITgcm_verif_basic     %  mv MITgcm MITgcm_verif_basic
157  \end{verbatim}  \end{verbatim}
158    
# Line 163  your copy instead of downloading the ent Line 166  your copy instead of downloading the ent
166  \end{verbatim}  \end{verbatim}
167  and then issue the cvs update command such as:  and then issue the cvs update command such as:
168  \begin{verbatim}  \begin{verbatim}
169  % cvs -q update -r checkpoint52i_post -d -P  % cvs -q update -d -P -r checkpoint52i_post
170  \end{verbatim}  \end{verbatim}
171  This will update the ``tag'' to ``checkpoint52i\_post'', add any new  This will update the ``tag'' to ``checkpoint52i\_post'', add any new
172  directories (-d) and remove any empty directories (-P). The -q option  directories (-d) and remove any empty directories (-P). The -q option
# Line 209  have run into a problem for which ``we h Line 212  have run into a problem for which ``we h
212  latest code'' and we haven't made a ``tag'' or ``release'' since that  latest code'' and we haven't made a ``tag'' or ``release'' since that
213  patch then you'll need to get the latest code:  patch then you'll need to get the latest code:
214  \begin{verbatim}  \begin{verbatim}
215  % cvs -q update -A -d -P  % cvs -q update -d -P -A
216  \end{verbatim}  \end{verbatim}
217  Unlike, the ``check-out'' and ``update'' procedures above, there is no  Unlike, the ``check-out'' and ``update'' procedures above, there is no
218  ``tag'' or release name. The -A tells CVS to upgrade to the  ``tag'' or release name. The -A tells CVS to upgrade to the
# Line 220  also means we can't tell what version of Line 223  also means we can't tell what version of
223  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
224    
225  \subsection{Method 2 - Tar file download}  \subsection{Method 2 - Tar file download}
226  \label{sect:conventionalDownload}  \label{sec:conventionalDownload}
227    
228  If you do not have CVS on your system, you can download the model as a  If you do not have CVS on your system, you can download the model as a
229  tar file from the web site at:  tar file from the web site at:
# Line 277  structure). Line 280  structure).
280    package corresponds to a subdirectory. For example, \texttt{gmredi}    package corresponds to a subdirectory. For example, \texttt{gmredi}
281    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
282    \texttt{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
283    physics. The packages are described in detail in chapter \ref{chap.packagesI}.    physics. The packages are described in detail in chapter \ref{chap:packagesI}.
284        
285  \item \texttt{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
286    For example, \texttt{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
# Line 301  structure). Line 304  structure).
304    decompositions.    decompositions.
305        
306  \item \texttt{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
307    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sec:modelExamples}.
308    
309  \item \texttt{jobs}: contains sample job scripts for running MITgcm.  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
310        
# Line 312  structure). Line 315  structure).
315  \end{itemize}  \end{itemize}
316    
317  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
318  \label{sect:buildingCode}  \label{sec:buildingCode}
319  \begin{rawhtml}  \begin{rawhtml}
320  <!-- CMIREDIR:buildingCode: -->  <!-- CMIREDIR:buildingCode: -->
321  \end{rawhtml}  \end{rawhtml}
# Line 321  To compile the code, we use the \texttt{ Line 324  To compile the code, we use the \texttt{
324  file (\texttt{Makefile}) that allows us to pre-process source files,  file (\texttt{Makefile}) that allows us to pre-process source files,
325  specify compiler and optimization options and also figures out any  specify compiler and optimization options and also figures out any
326  file dependencies. We supply a script (\texttt{genmake2}), described  file dependencies. We supply a script (\texttt{genmake2}), described
327  in section \ref{sect:genmake}, that automatically creates the  in section \ref{sec:genmake}, that automatically creates the
328  \texttt{Makefile} for you. You then need to build the dependencies and  \texttt{Makefile} for you. You then need to build the dependencies and
329  compile the code.  compile the code.
330    
# Line 396  where the ``2'' can be replaced with a n Line 399  where the ``2'' can be replaced with a n
399  number of CPUs available.  number of CPUs available.
400    
401  Now you are ready to run the model. General instructions for doing so are  Now you are ready to run the model. General instructions for doing so are
402  given in section \ref{sect:runModel}. Here, we can run the model by  given in section \ref{sec:runModel}. Here, we can run the model by
403  first creating links to all the input files:  first creating links to all the input files:
404  \begin{verbatim}  \begin{verbatim}
405  ln -s ../input/* .  ln -s ../input/* .
# Line 410  where we are re-directing the stream of Line 413  where we are re-directing the stream of
413    
414  \subsection{Building/compiling the code elsewhere}  \subsection{Building/compiling the code elsewhere}
415    
416  In the example above (section \ref{sect:buildingCode}) we built the  In the example above (section \ref{sec:buildingCode}) we built the
417  executable in the {\em input} directory of the experiment for  executable in the {\em input} directory of the experiment for
418  convenience. You can also configure and compile the code in other  convenience. You can also configure and compile the code in other
419  locations, for example on a scratch disk with out having to copy the  locations, for example on a scratch disk with out having to copy the
# Line 514  the one experiment: Line 517  the one experiment:
517    
518    
519  \subsection{Using \texttt{genmake2}}  \subsection{Using \texttt{genmake2}}
520  \label{sect:genmake}  \label{sec:genmake}
521    
522  To compile the code, first use the program \texttt{genmake2} (located  To compile the code, first use the program \texttt{genmake2} (located
523  in the \texttt{tools} directory) to generate a Makefile.  in the \texttt{tools} directory) to generate a Makefile.
# Line 685  The most important command-line options Line 688  The most important command-line options
688        
689  \item[\texttt{--mpi}] This option enables certain MPI features (using  \item[\texttt{--mpi}] This option enables certain MPI features (using
690    CPP \texttt{\#define}s) within the code and is necessary for MPI    CPP \texttt{\#define}s) within the code and is necessary for MPI
691    builds (see Section \ref{sect:mpi-build}).    builds (see Section \ref{sec:mpi-build}).
692        
693  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
694    soft-links and other bugs common with the \texttt{make} versions    soft-links and other bugs common with the \texttt{make} versions
# Line 708  The most important command-line options Line 711  The most important command-line options
711    
712    
713  \subsection{Building with MPI}  \subsection{Building with MPI}
714  \label{sect:mpi-build}  \label{sec:mpi-build}
715    
716  Building MITgcm to use MPI libraries can be complicated due to the  Building MITgcm to use MPI libraries can be complicated due to the
717  variety of different MPI implementations available, their dependencies  variety of different MPI implementations available, their dependencies
# Line 723  The steps for building MITgcm with MPI s Line 726  The steps for building MITgcm with MPI s
726        
727  \item Determine the locations of your MPI-enabled compiler and/or MPI  \item Determine the locations of your MPI-enabled compiler and/or MPI
728    libraries and put them into an options file as described in Section    libraries and put them into an options file as described in Section
729    \ref{sect:genmake}.  One can start with one of the examples in:    \ref{sec:genmake}.  One can start with one of the examples in:
730    \begin{rawhtml} <A    \begin{rawhtml} <A
731      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
732    \end{rawhtml}    \end{rawhtml}
# Line 758  The steps for building MITgcm with MPI s Line 761  The steps for building MITgcm with MPI s
761    \end{itemize}    \end{itemize}
762        
763  \item Build the code with the \texttt{genmake2} \texttt{-mpi} option  \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
764    (see Section \ref{sect:genmake}) using commands such as:    (see Section \ref{sec:genmake}) using commands such as:
765  {\footnotesize \begin{verbatim}  {\footnotesize \begin{verbatim}
766    %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE    %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
767    %  make depend    %  make depend
# Line 812  the GNU g77 compiler and the mpich MPI l Line 815  the GNU g77 compiler and the mpich MPI l
815  \end{verbatim} }  \end{verbatim} }
816    
817  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
818  \label{sect:runModel}  \label{sec:runModel}
819  \begin{rawhtml}  \begin{rawhtml}
820  <!-- CMIREDIR:runModel: -->  <!-- CMIREDIR:runModel: -->
821  \end{rawhtml}  \end{rawhtml}
822    
823  If compilation finished succesfully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sec:buildingCode})
824  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
825  local directory.  local directory.
826    
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