/[MITgcm]/manual/s_getstarted/text/getting_started.tex

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-revision 1.42 by jmc,
Fri May 28 02:09:59 2010 UTC
+revision 1.47 by jmc,
Tue Jan  9 01:02:48 2018 UTC
 Line 8 
 model is to run the case study examples
  version. Information on how to obtain, compile, and run the code is
  found here as well as a brief description of the model structure
  directory and the case study examples. Information is also provided
  here on how to customize the code when you are ready to try implementing
  the configuration you have in mind.  The code and algorithm
  are described more fully in chapters \ref{chap:discretization} and
  \ref{chap:sarch}.
  \section{Where to find information}
- \label{sect:whereToFindInfo}
+ \label{sec:whereToFindInfo}
  \begin{rawhtml}
  <!-- CMIREDIR:whereToFindInfo: -->
  \end{rawhtml}
  There is a web-archived support mailing list for the model that
- you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
+ you can email at \texttt{MITgcm-support@mitgcm.org} after subscribing to:
- \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
+ \begin{rawhtml} <A href=http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
  \begin{verbatim}
- http://mitgcm.org/mailman/listinfo/mitgcm-support/
+ http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support/
- http://mitgcm.org/pipermail/mitgcm-support/
+ \end{verbatim}
+ \begin{rawhtml} </A> \end{rawhtml}
+ or browse at:
+ \begin{rawhtml} <A href=http://mailman.mitgcm.org/pipermail/mitgcm-support/ target="idontexist"> \end{rawhtml}
+ \begin{verbatim}
+ http://mailman.mitgcm.org/pipermail/mitgcm-support/
  \end{verbatim}
  \begin{rawhtml} </A> \end{rawhtml}
  \section{Obtaining the code}
- \label{sect:obtainingCode}
+ \label{sec:obtainingCode}
  \begin{rawhtml}
  <!-- CMIREDIR:obtainingCode: -->
  \end{rawhtml}
-Line 63 
 provide easy support for maintenance upd
+Line 68 
 provide easy support for maintenance upd
  \end{enumerate}
  \subsection{Method 1 - Checkout from CVS}
- \label{sect:cvs_checkout}
+ \label{sec:cvs_checkout}
  If CVS is available on your system, we strongly encourage you to use it. CVS
  provides an efficient and elegant way of organizing your code and keeping
-Line 71 
 track of your changes. If CVS is not ava
+Line 76 
 track of your changes. If CVS is not ava
  download a tar file.
  Before you can use CVS, the following environment variable(s) should
  be set within your shell.  For a csh or tcsh shell, put the following
  \begin{verbatim}
  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
  \end{verbatim}
-Line 82 
 shells, put:
+Line 87 
 shells, put:
  \end{verbatim}
  in your \texttt{.profile} or \texttt{.bashrc} file.
  To get MITgcm through CVS, first register with the MITgcm CVS server
  using command:
  \begin{verbatim}
-Line 92 
 You only need to do a ``cvs login'' once
+Line 96 
 You only need to do a ``cvs login'' once
  To obtain the latest sources type:
  \begin{verbatim}
- % cvs co MITgcm
+ % cvs co -P MITgcm
  \end{verbatim}
  or to get a specific release type:
  \begin{verbatim}
- % cvs co -P -r checkpoint52i_post  MITgcm
+ % cvs co -P -r checkpoint52i_post MITgcm
  \end{verbatim}
+ The CVS command ``\texttt{cvs co}'' is the abreviation of the full-name
+ ``\texttt{cvs checkout}'' command and using the option ``-P'' (\texttt{cvs co -P})
+ will prevent to download unnecessary empty directories.
  The MITgcm web site contains further directions concerning the source
  code and CVS.  It also contains a web interface to our CVS archive so
  that one may easily view the state of files, revisions, and other
  development milestones:
- %\begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
  \begin{rawhtml} <A href="http://mitgcm.org/viewvc/MITgcm/MITgcm/" target="idontexist"> \end{rawhtml}
  \begin{verbatim}
- http://mitgcm.org/source_code.html
+ http://mitgcm.org/viewvc/MITgcm/MITgcm/
  \end{verbatim}
  \begin{rawhtml} </A> \end{rawhtml}
-Line 120 
 of CVS aliases
+Line 127 
 of CVS aliases
      \textbf{Alias Name}    &  \textbf{Information (directories) Contained}  \\\hline
      \texttt{MITgcm\_code}  &  Only the source code -- none of the verification examples.  \\
      \texttt{MITgcm\_verif\_basic}
      &  Source code plus a small set of the verification examples
      (\texttt{global\_ocean.90x40x15}, \texttt{aim.5l\_cs}, \texttt{hs94.128x64x5},
      \texttt{front\_relax}, and \texttt{plume\_on\_slope}).  \\
      \texttt{MITgcm\_verif\_atmos}  &  Source code plus all of the atmospheric examples.  \\
      \texttt{MITgcm\_verif\_ocean}  &  Source code plus all of the oceanic examples.  \\
-Line 142 
 updates.  More extensive information on
+Line 149 
 updates.  More extensive information on
  MITgcm code can be found
  \begin{rawhtml} <A href="http://mitgcm.org/public/using_cvs.html" target="idontexist"> \end{rawhtml}
  here
- \begin{rawhtml} </A> \end{rawhtml}
+ \begin{rawhtml} </A> \end{rawhtml}.
- .
  It is important to note that the CVS aliases in Table
  \ref{tab:cvsModules} cannot be used in conjunction with the CVS
  \texttt{-d DIRNAME} option.  However, the \texttt{MITgcm} directories
  they create can be changed to a different name following the check-out:
  \begin{verbatim}
-    %  cvs co MITgcm_verif_basic
+    %  cvs co -P MITgcm_verif_basic
     %  mv MITgcm MITgcm_verif_basic
  \end{verbatim}
+ Note that it is possible to checkout code without ``cvs login'' and without
+ setting any shell environment variables by specifying the pserver name and
+ password in one line, for example:
+ \begin{verbatim}
+    %  cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -P MITgcm
+ \end{verbatim}
  \subsubsection{Upgrading from an earlier version}
  If you already have an earlier version of the code you can ``upgrade''
-Line 163 
 your copy instead of downloading the ent
+Line 176 
 your copy instead of downloading the ent
  \end{verbatim}
  and then issue the cvs update command such as:
  \begin{verbatim}
- % cvs -q update -r checkpoint52i_post -d -P
+ % cvs -q update -d -P -r checkpoint52i_post
  \end{verbatim}
  This will update the ``tag'' to ``checkpoint52i\_post'', add any new
  directories (-d) and remove any empty directories (-P). The -q option
-Line 209 
 have run into a problem for which ``we h
+Line 222 
 have run into a problem for which ``we h
  latest code'' and we haven't made a ``tag'' or ``release'' since that
  patch then you'll need to get the latest code:
  \begin{verbatim}
- % cvs -q update -A -d -P
+ % cvs -q update -d -P -A
  \end{verbatim}
  Unlike, the ``check-out'' and ``update'' procedures above, there is no
  ``tag'' or release name. The -A tells CVS to upgrade to the
-Line 220 
 also means we can't tell what version of
+Line 233 
 also means we can't tell what version of
  with. So please be sure you understand what you're doing.
  \subsection{Method 2 - Tar file download}
- \label{sect:conventionalDownload}
+ \label{sec:conventionalDownload}
  If you do not have CVS on your system, you can download the model as a
  tar file from the web site at:
-Line 233 
 The tar file still contains CVS informat
+Line 246 
 The tar file still contains CVS informat
  delete; even if you do not use CVS yourself the information can help
  us if you should need to send us your copy of the code.  If a recent
  tar file does not exist, then please contact the developers through
  the
  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
  MITgcm-support@mitgcm.org
  \begin{rawhtml} </A> \end{rawhtml}
-Line 264 
 structure).
+Line 277 
 structure).
  \begin{itemize}
  \item \texttt{doc}: contains brief documentation notes.
  \item \texttt{eesupp}: contains the execution environment source code.
    Also subdivided into two subdirectories \texttt{inc} and
    \texttt{src}.
  \item \texttt{model}: this directory contains the main source code.
    Also subdivided into two subdirectories \texttt{inc} and
    \texttt{src}.
  \item \texttt{pkg}: contains the source code for the packages. Each
    package corresponds to a subdirectory. For example, \texttt{gmredi}
    contains the code related to the Gent-McWilliams/Redi scheme,
    \texttt{aim} the code relative to the atmospheric intermediate
-   physics. The packages are described in detail in chapter \ref{chap.packagesI}.
+   physics. The packages are described in detail in chapter \ref{chap:packagesI}.
  \item \texttt{tools}: this directory contains various useful tools.
    For example, \texttt{genmake2} is a script written in csh (C-shell)
    that should be used to generate your makefile. The directory
-Line 288 
 structure).
+Line 301 
 structure).
    This directory also contains the subdirectory build\_options, which
    contains the `optfiles' with the compiler options for the different
    compilers and machines that can run MITgcm.
  \item \texttt{utils}: this directory contains various utilities. The
    subdirectory \texttt{knudsen2} contains code and a makefile that
    compute coefficients of the polynomial approximation to the knudsen
-Line 299 
 structure).
+Line 312 
 structure).
    model output. The subdirectory exch2 contains the code needed for
    the exch2 package to work with different combinations of domain
    decompositions.
  \item \texttt{verification}: this directory contains the model
-   examples. See section \ref{sect:modelExamples}.
+   examples. See section \ref{sec:modelExamples}.
  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
  \item \texttt{lsopt}: Line search code used for optimization.
  \item \texttt{optim}: Interface between MITgcm and line search code.
  \end{itemize}
  \section[Building MITgcm]{Building the code}
- \label{sect:buildingCode}
+ \label{sec:buildingCode}
  \begin{rawhtml}
  <!-- CMIREDIR:buildingCode: -->
  \end{rawhtml}
-Line 321 
 To compile the code, we use the \texttt{
+Line 334 
 To compile the code, we use the \texttt{
  file (\texttt{Makefile}) that allows us to pre-process source files,
  specify compiler and optimization options and also figures out any
  file dependencies. We supply a script (\texttt{genmake2}), described
- in section \ref{sect:genmake}, that automatically creates the
+ in section \ref{sec:genmake}, that automatically creates the
  \texttt{Makefile} for you. You then need to build the dependencies and
  compile the code.
-Line 353 
 MITgcm.  In such cases, it is generally
+Line 366 
 MITgcm.  In such cases, it is generally
  Through the MITgcm-support list, the MITgcm developers are willing to
  provide help writing or modifing ``optfiles''.  And we encourage users
  to post new ``optfiles'' (particularly ones for new machines or
  architectures) to the
  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
  MITgcm-support@mitgcm.org
  \begin{rawhtml} </A> \end{rawhtml}
-Line 396 
 where the ``2'' can be replaced with a n
+Line 409 
 where the ``2'' can be replaced with a n
  number of CPUs available.
  Now you are ready to run the model. General instructions for doing so are
- 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
  first creating links to all the input files:
  \begin{verbatim}
  ln -s ../input/* .
-Line 410 
 where we are re-directing the stream of
+Line 423 
 where we are re-directing the stream of
  \subsection{Building/compiling the code elsewhere}
- In the example above (section \ref{sect:buildingCode}) we built the
+ In the example above (section \ref{sec:buildingCode}) we built the
  executable in the {\em input} directory of the experiment for
  convenience. You can also configure and compile the code in other
  locations, for example on a scratch disk with out having to copy the
-Line 512 
 the one experiment:
+Line 525 
 the one experiment:
  % ./mitgcmuv > output.txt
  \end{verbatim}
  \subsection{Using \texttt{genmake2}}
- \label{sect:genmake}
+ \label{sec:genmake}
  To compile the code, first use the program \texttt{genmake2} (located
  in the \texttt{tools} directory) to generate a Makefile.
-Line 526 
 in the \texttt{tools} directory) to gene
+Line 538 
 in the \texttt{tools} directory) to gene
  %\texttt{tools/build\_options} directory.
  \texttt{genmake2} parses information from the following sources:
  \begin{description}
  \item[-] a {\em gemake\_local} file if one is found in the current
    directory
  \item[-] command-line options
  \item[-] an "options file" as specified by the command-line option
    \texttt{--optfile=/PATH/FILENAME}
  \item[-] a {\em packages.conf} file (if one is found) with the
    specific list of packages to compile. The search path for
    file {\em packages.conf} is, first, the current directory and
    then each of the "MODS" directories in the given order (see below).
  \end{description}
-Line 621 
 obtained from:
+Line 633 
 obtained from:
  The most important command-line options are:
  \begin{description}
  \item[\texttt{--optfile=/PATH/FILENAME}] specifies the optfile that
    should be used for a particular build.
    If no "optfile" is specified (either through the command line or the
    MITGCM\_OPTFILE environment variable), genmake2 will try to make a
    reasonable guess from the list provided in {\em
-Line 633 
 The most important command-line options
+Line 645 
 The most important command-line options
    (eg. "linux\_ia32") and then find a working FORTRAN compiler within
    the user's path.  When these three items have been identified,
    genmake2 will try to find an optfile that has a matching name.
  \item[\texttt{--mods='DIR1 DIR2 DIR3 ...'}] specifies a list of
    directories containing ``modifications''.  These directories contain
    files with names that may (or may not) exist in the main MITgcm
    source tree but will be overridden by any identically-named sources
    within the ``MODS'' directories.
    The order of precedence for this "name-hiding" is as follows:
    \begin{itemize}
    \item ``MODS'' directories (in the order given)
-Line 650 
 The most important command-line options
+Line 662 
 The most important command-line options
    \item The "standard dirs" (which may have been specified by the
      ``-standarddirs'' option)
    \end{itemize}
  \item[\texttt{--pgroups=/PATH/FILENAME}] specifies the file
    where package groups are defined. If not set, the package-groups
    definition will be read from {\em pkg/pkg\_groups}.
    It also contains the default list of packages (defined
    as the group ``{\it default\_pkg\_list}'' which is used
-Line 661 
 The most important command-line options
+Line 673 
 The most important command-line options
  \item[\texttt{--pdepend=/PATH/FILENAME}] specifies the dependency file
    used for packages.
    If not specified, the default dependency file {\em pkg/pkg\_depend}
    is used.  The syntax for this file is parsed on a line-by-line basis
    where each line containes either a comment ("\#") or a simple
-Line 670 
 The most important command-line options
+Line 682 
 The most important command-line options
    relationship, respectively.  If no rule is specified, then it is
    assumed that the two packages are compatible and will function
    either with or without each other.
  \item[\texttt{--adof=/path/to/file}] specifies the "adjoint" or
    automatic differentiation options file to be used.  The file is
    analogous to the ``optfile'' defined above but it specifies
    information for the AD build process.
    The default file is located in {\em
      tools/adjoint\_options/adjoint\_default} and it defines the "TAF"
    and "TAMC" compilers.  An alternate version is also available at
    {\em tools/adjoint\_options/adjoint\_staf} that selects the newer
    "STAF" compiler.  As with any compilers, it is helpful to have their
    directories listed in your {\tt \$PATH} environment variable.
  \item[\texttt{--mpi}] This option enables certain MPI features (using
    CPP \texttt{\#define}s) within the code and is necessary for MPI
-   builds (see Section \ref{sect:mpi-build}).
+   builds (see Section \ref{sec:mpi-build}).
  \item[\texttt{--make=/path/to/gmake}] Due to the poor handling of
    soft-links and other bugs common with the \texttt{make} versions
    provided by commercial Unix vendors, GNU \texttt{make} (sometimes
    called \texttt{gmake}) should be preferred.  This option provides a
    means for specifying the make executable to be used.
  \item[\texttt{--bash=/path/to/sh}] On some (usually older UNIX)
    machines, the ``bash'' shell is unavailable.  To run on these
    systems, \texttt{genmake2} can be invoked using an ``sh'' (that is,
-Line 706 
 The most important command-line options
+Line 718 
 The most important command-line options
  \end{description}
  \subsection{Building with MPI}
- \label{sect:mpi-build}
+ \label{sec:mpi-build}
  Building MITgcm to use MPI libraries can be complicated due to the
  variety of different MPI implementations available, their dependencies
-Line 720 
 administrator.
+Line 731 
 administrator.
  The steps for building MITgcm with MPI support are:
  \begin{enumerate}
  \item Determine the locations of your MPI-enabled compiler and/or MPI
    libraries and put them into an options file as described in Section
-   \ref{sect:genmake}.  One can start with one of the examples in:
+   \ref{sec:genmake}.  One can start with one of the examples in:
    \begin{rawhtml} <A
      href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
    \end{rawhtml}
-Line 756 
 The steps for building MITgcm with MPI s
+Line 767 
 The steps for building MITgcm with MPI s
      MPIexec
      \begin{rawhtml} </A> \end{rawhtml}
    \end{itemize}
  \item Build the code with the \texttt{genmake2} \texttt{-mpi} option
-   (see Section \ref{sect:genmake}) using commands such as:
+   (see Section \ref{sec:genmake}) using commands such as:
  {\footnotesize \begin{verbatim}
    %  ../../../tools/genmake2 -mods=../code -mpi -of=YOUR_OPTFILE
    %  make depend
    %  make
  \end{verbatim} }
  \item Run the code with the appropriate MPI ``run'' or ``exec''
    program provided with your particular implementation of MPI.
    Typical MPI packages such as MPICH will use something like:
-Line 812 
 the GNU g77 compiler and the mpich MPI l
+Line 823 
 the GNU g77 compiler and the mpich MPI l
  \end{verbatim} }
  \section[Running MITgcm]{Running the model in prognostic mode}
- \label{sect:runModel}
+ \label{sec:runModel}
  \begin{rawhtml}
  <!-- CMIREDIR:runModel: -->
  \end{rawhtml}
- If compilation finished succesfully (section \ref{sect:buildingCode})
+ If compilation finished succesfully (section \ref{sec:buildingCode})
  then an executable called \texttt{mitgcmuv} will now exist in the
  local directory.
-Line 845 
 output is kept in \texttt{results/output
+Line 856 
 output is kept in \texttt{results/output
  compare your \texttt{output.txt} with the corresponding one for that
  experiment to check that the set-up works.
  \subsection{Output files}
  The model produces various output files and, when using \texttt{mnc},
-Line 856 
 both as determined by \texttt{code/packa
+Line 865 
 both as determined by \texttt{code/packa
  flags set (in \texttt{input/data.pkg}), the following output may
  appear.
  \subsubsection{MDSIO output files}
  The ``traditional'' output files are generated by the \texttt{mdsio}
-Line 904 
 there is an additional ``pickup'' file:
+Line 912 
 there is an additional ``pickup'' file:
  containing the D-grid velocity data and that has to be written out as well
  in order to restart the integration. Rolling checkpoint files are the same
  as the pickup files but are named differently. Their name contain the chain
  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
  used to restart the model but are overwritten every other time they are
  output to save disk space during long integrations.
-Line 913 
 output to save disk space during long in
+Line 921 
 output to save disk space during long in
  Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
  is usually (though not necessarily) placed within a subdirectory with
  a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.
  \subsection{Looking at the output}
-Line 968 
 http://www.unidata.ucar.edu/packages/net
+Line 976 
 http://www.unidata.ucar.edu/packages/net
  http://meteora.ucsd.edu/~pierce/ncview_home_page.html
  \end{verbatim}
    \begin{rawhtml} </A> \end{rawhtml}
  \item MatLAB(c) and other common post-processing environments provide
    various netCDF interfaces including:
    \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}

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