/[MITgcm]/manual/s_getstarted/text/getting_started.tex
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revision 1.23 by edhill, Thu Apr 8 02:24:23 2004 UTC revision 1.26 by cnh, Wed Oct 13 05:06:25 2004 UTC
# Line 324  structure). Line 324  structure).
324    
325  \end{itemize}  \end{itemize}
326    
327  \section{Example experiments}  \section[MITgcm Example Experiments]{Example experiments}
328  \label{sect:modelExamples}  \label{sect:modelExamples}
329    
330  %% a set of twenty-four pre-configured numerical experiments  %% a set of twenty-four pre-configured numerical experiments
# Line 484  Each example directory has the following Line 484  Each example directory has the following
484  Once you have chosen the example you want to run, you are ready to  Once you have chosen the example you want to run, you are ready to
485  compile the code.  compile the code.
486    
487  \section{Building the code}  \section[Building MITgcm]{Building the code}
488  \label{sect:buildingCode}  \label{sect:buildingCode}
489    
490  To compile the code, we use the {\em make} program. This uses a file  To compile the code, we use the {\em make} program. This uses a file
# Line 666  the one experiment: Line 666  the one experiment:
666  \end{verbatim}  \end{verbatim}
667    
668    
669  \subsection{Using \textit{genmake2}}  \subsection{Using \texttt{genmake2}}
670  \label{sect:genmake}  \label{sect:genmake}
671    
672  To compile the code, first use the program \texttt{genmake2} (located  To compile the code, first use the program \texttt{genmake2} (located
673  in the \textit{tools} directory) to generate a Makefile.  in the \texttt{tools} directory) to generate a Makefile.
674  \texttt{genmake2} is a shell script written to work with all  \texttt{genmake2} is a shell script written to work with all
675  ``sh''--compatible shells including bash v1, bash v2, and Bourne.  ``sh''--compatible shells including bash v1, bash v2, and Bourne.
676  Internally, \texttt{genmake2} determines the locations of needed  Internally, \texttt{genmake2} determines the locations of needed
677  files, the compiler, compiler options, libraries, and Unix tools.  It  files, the compiler, compiler options, libraries, and Unix tools.  It
678  relies upon a number of ``optfiles'' located in the {\em  relies upon a number of ``optfiles'' located in the
679    tools/build\_options} directory.  \texttt{tools/build\_options} directory.
680    
681  The purpose of the optfiles is to provide all the compilation options  The purpose of the optfiles is to provide all the compilation options
682  for particular ``platforms'' (where ``platform'' roughly means the  for particular ``platforms'' (where ``platform'' roughly means the
# Line 918  The steps for building MITgcm with MPI s Line 918  The steps for building MITgcm with MPI s
918    Sightly more complicated scripts may be needed for many machines    Sightly more complicated scripts may be needed for many machines
919    since execution of the code may be controlled by both the MPI    since execution of the code may be controlled by both the MPI
920    library and a job scheduling and queueing system such as PBS,    library and a job scheduling and queueing system such as PBS,
921    LoadLeveller, Condor, or any of a number of similar tools.    LoadLeveller, Condor, or any of a number of similar tools.  A few
922      example scripts (those used for our \begin{rawhtml} <A
923        href="http://mitgcm.org/testing.html"> \end{rawhtml}regular
924      verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
925      at:
926      \begin{rawhtml} <A
927        href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
928      \end{rawhtml}
929      {\footnotesize \tt
930        http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }
931      \begin{rawhtml} </A> \end{rawhtml}
932    
933  \end{enumerate}  \end{enumerate}
934    
935    An example of the above process on the MITgcm cluster (``cg01'') using
936    the GNU g77 compiler and the mpich MPI library is:
937    
938    {\footnotesize \begin{verbatim}
939      %  cd MITgcm/verification/exp5
940      %  mkdir build
941      %  cd build
942      %  ../../../tools/genmake2 -mpi -mods=../code \
943           -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
944      %  make depend
945      %  make
946      %  cd ../input
947      %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
948           -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
949    \end{verbatim} }
950    
951    
952    
953  \section{Running the model}  \section[Running MITgcm]{Running the model in prognostic mode}
954  \label{sect:runModel}  \label{sect:runModel}
955    
956  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfuully (section \ref{sect:buildingCode})
# Line 1033  Some examples of reading and visualizing Line 1059  Some examples of reading and visualizing
1059  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
1060  \end{verbatim}  \end{verbatim}
1061    
1062  \section{Doing it yourself: customizing the code}  \section[Customizing MITgcm]{Doing it yourself: customizing the code}
1063    
1064  When you are ready to run the model in the configuration you want, the  When you are ready to run the model in the configuration you want, the
1065  easiest thing is to use and adapt the setup of the case studies  easiest thing is to use and adapt the setup of the case studies
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