/[MITgcm]/manual/s_getstarted/text/getting_started.tex
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revision 1.18 by edhill, Thu Jan 29 19:22:35 2004 UTC revision 1.23 by edhill, Thu Apr 8 02:24:23 2004 UTC
# Line 79  provide easy support for maintenance upd Line 79  provide easy support for maintenance upd
79    
80  \end{enumerate}  \end{enumerate}
81    
82    \subsubsection{Checkout from CVS}
83    \label{sect:cvs_checkout}
84    
85  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
86  provides an efficient and elegant way of organizing your code and keeping  provides an efficient and elegant way of organizing your code and keeping
87  track of your changes. If CVS is not available on your machine, you can also  track of your changes. If CVS is not available on your machine, you can also
# Line 93  in your .cshrc or .tcshrc file.  For bas Line 96  in your .cshrc or .tcshrc file.  For bas
96  \begin{verbatim}  \begin{verbatim}
97  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
98  \end{verbatim}  \end{verbatim}
99  in your .profile or .bashrc file.  in your \texttt{.profile} or \texttt{.bashrc} file.
100    
101    
102  To get MITgcm through CVS, first register with the MITgcm CVS server  To get MITgcm through CVS, first register with the MITgcm CVS server
# Line 121  http://mitgcm.org/source_code.html Line 124  http://mitgcm.org/source_code.html
124  \end{verbatim}  \end{verbatim}
125  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
126    
127    As a convenience, the MITgcm CVS server contains aliases which are
128    named subsets of the codebase.  These aliases can be especially
129    helpful when used over slow internet connections or on machines with
130    restricted storage space.  Table \ref{tab:cvsModules} contains a list
131    of CVS aliases
132    \begin{table}[htb]
133      \centering
134      \begin{tabular}[htb]{|lp{3.25in}|}\hline
135        \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline
136        \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\
137        \texttt{MITgcm\_verif\_basic}
138        &  Source code plus a small set of the verification examples
139        (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5},
140        \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\
141        \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\
142        \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\
143        \texttt{MITgcm\_verif\_all}    &  Source code plus all of the
144        verification examples. \\\hline
145      \end{tabular}
146      \caption{MITgcm CVS Modules}
147      \label{tab:cvsModules}
148    \end{table}
149    
150  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \textit{MITgcm}. If
151  the directory \textit{MITgcm} exists this command updates your code  the directory \textit{MITgcm} exists this command updates your code
# Line 134  MITgcm code can be found Line 159  MITgcm code can be found
159  here  here
160  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
161  .  .
162    It is important to note that the CVS aliases in Table
163    \ref{tab:cvsModules} cannot be used in conjunction with the CVS
164    \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
165    they create can be changed to a different name following the check-out:
166    \begin{verbatim}
167       %  cvs co MITgcm_verif_basic
168       %  mv MITgcm MITgcm_verif_basic
169    \end{verbatim}
170    
171    
172  \paragraph*{Conventional download method}  \subsubsection{Conventional download method}
173  \label{sect:conventionalDownload}  \label{sect:conventionalDownload}
174    
175  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
# Line 156  MITgcm-support@mitgcm.org Line 189  MITgcm-support@mitgcm.org
189  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
190  mailing list.  mailing list.
191    
192  \paragraph*{Upgrading from an earlier version}  \subsubsection{Upgrading from an earlier version}
193    
194  If you already have an earlier version of the code you can ``upgrade''  If you already have an earlier version of the code you can ``upgrade''
195  your copy instead of downloading the entire repository again. First,  your copy instead of downloading the entire repository again. First,
# Line 633  the one experiment: Line 666  the one experiment:
666  \end{verbatim}  \end{verbatim}
667    
668    
   
669  \subsection{Using \textit{genmake2}}  \subsection{Using \textit{genmake2}}
670  \label{sect:genmake}  \label{sect:genmake}
671    
# Line 739  The most important command-line options Line 771  The most important command-line options
771    the user's path.  When these three items have been identified,    the user's path.  When these three items have been identified,
772    genmake2 will try to find an optfile that has a matching name.    genmake2 will try to find an optfile that has a matching name.
773        
774    \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
775      set of packages to be used.  The normal order of precedence for
776      packages is as follows:
777      \begin{enumerate}
778      \item If available, the command line (\texttt{--pdefault}) settings
779        over-rule any others.
780    
781      \item Next, \texttt{genmake2} will look for a file named
782        ``\texttt{packages.conf}'' in the local directory or in any of the
783        directories specified with the \texttt{--mods} option.
784        
785      \item Finally, if neither of the above are available,
786        \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
787      \end{enumerate}
788      
789  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
790    used for packages.    used for packages.
791        
# Line 751  The most important command-line options Line 798  The most important command-line options
798    assumed that the two packages are compatible and will function    assumed that the two packages are compatible and will function
799    either with or without each other.    either with or without each other.
800        
 \item[\texttt{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default  
   set of packages to be used.  
     
   If not set, the default package list will be read from {\em  
     pkg/pkg\_default}  
     
801  \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or  \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
802    automatic differentiation options file to be used.  The file is    automatic differentiation options file to be used.  The file is
803    analogous to the ``optfile'' defined above but it specifies    analogous to the ``optfile'' defined above but it specifies
# Line 786  The most important command-line options Line 827  The most important command-line options
827      ``-standarddirs'' option)      ``-standarddirs'' option)
828    \end{itemize}    \end{itemize}
829        
830    \item[\texttt{--mpi}] This option enables certain MPI features (using
831      CPP \texttt{\#define}s) within the code and is necessary for MPI
832      builds (see Section \ref{sect:mpi-build}).
833      
834  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
835    soft-links and other bugs common with the \texttt{make} versions    soft-links and other bugs common with the \texttt{make} versions
836    provided by commercial Unix vendors, GNU \texttt{make} (sometimes    provided by commercial Unix vendors, GNU \texttt{make} (sometimes
837    called \texttt{gmake}) should be preferred.  This option provides a    called \texttt{gmake}) should be preferred.  This option provides a
838    means for specifying the make executable to be used.    means for specifying the make executable to be used.
839      
840    \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
841      machines, the ``bash'' shell is unavailable.  To run on these
842      systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
843      a Bourne, POSIX, or compatible) shell.  The syntax in these
844      circumstances is:
845      \begin{center}
846        \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
847      \end{center}
848      where \texttt{/bin/sh} can be replaced with the full path and name
849      of the desired shell.
850    
851  \end{description}  \end{description}
852    
853    
854    \subsection{Building with MPI}
855    \label{sect:mpi-build}
856    
857    Building MITgcm to use MPI libraries can be complicated due to the
858    variety of different MPI implementations available, their dependencies
859    or interactions with different compilers, and their often ad-hoc
860    locations within file systems.  For these reasons, its generally a
861    good idea to start by finding and reading the documentation for your
862    machine(s) and, if necessary, seeking help from your local systems
863    administrator.
864    
865    The steps for building MITgcm with MPI support are:
866    \begin{enumerate}
867      
868    \item Determine the locations of your MPI-enabled compiler and/or MPI
869      libraries and put them into an options file as described in Section
870      \ref{sect:genmake}.  One can start with one of the examples in:
871      \begin{rawhtml} <A
872        href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">
873      \end{rawhtml}
874      \begin{center}
875        \texttt{MITgcm/tools/build\_options/}
876      \end{center}
877      \begin{rawhtml} </A> \end{rawhtml}
878      such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
879      \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
880      hand.  You may need help from your user guide or local systems
881      administrator to determine the exact location of the MPI libraries.
882      If libraries are not installed, MPI implementations and related
883      tools are available including:
884      \begin{itemize}
885      \item \begin{rawhtml} <A
886          href="http://www-unix.mcs.anl.gov/mpi/mpich/">
887        \end{rawhtml}
888        MPICH
889        \begin{rawhtml} </A> \end{rawhtml}
890    
891      \item \begin{rawhtml} <A
892          href="http://www.lam-mpi.org/">
893        \end{rawhtml}
894        LAM/MPI
895        \begin{rawhtml} </A> \end{rawhtml}
896    
897      \item \begin{rawhtml} <A
898          href="http://www.osc.edu/~pw/mpiexec/">
899        \end{rawhtml}
900        MPIexec
901        \begin{rawhtml} </A> \end{rawhtml}
902      \end{itemize}
903      
904    \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
905      (see Section \ref{sect:genmake}) using commands such as:
906    {\footnotesize \begin{verbatim}
907      %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
908      %  make depend
909      %  make
910    \end{verbatim} }
911      
912    \item Run the code with the appropriate MPI ``run'' or ``exec''
913      program provided with your particular implementation of MPI.
914      Typical MPI packages such as MPICH will use something like:
915    \begin{verbatim}
916      %  mpirun -np 4 -machinefile mf ./mitgcmuv
917    \end{verbatim}
918      Sightly more complicated scripts may be needed for many machines
919      since execution of the code may be controlled by both the MPI
920      library and a job scheduling and queueing system such as PBS,
921      LoadLeveller, Condor, or any of a number of similar tools.
922    
923    \end{enumerate}
924    
925    
926    
927  \section{Running the model}  \section{Running the model}
928  \label{sect:runModel}  \label{sect:runModel}
929    
930  If compilation finished succesfuully (section \ref{sect:buildModel})  If compilation finished succesfuully (section \ref{sect:buildingCode})
931  then an executable called {\em mitgcmuv} will now exist in the local  then an executable called \texttt{mitgcmuv} will now exist in the
932  directory.  local directory.
933    
934  To run the model as a single process (ie. not in parallel) simply  To run the model as a single process (ie. not in parallel) simply
935  type:  type:
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