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--- manual/s_getstarted/text/getting_started.tex 2015/11/21 03:19:54 1.46
+++ manual/s_getstarted/text/getting_started.tex 2018/01/09 01:02:48 1.47
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.46 2015/11/21 03:19:54 dimitri Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.47 2018/01/09 01:02:48 jmc Exp $
% $Name: $
%\section{Getting started}
@@ -8,10 +8,10 @@
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
+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}.
+are described more fully in chapters \ref{chap:discretization} and
+\ref{chap:sarch}.
\section{Where to find information}
\label{sec:whereToFindInfo}
@@ -20,11 +20,16 @@
\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:
-\begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
+you can email at \texttt{MITgcm-support@mitgcm.org} after subscribing to:
+\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://mitgcm.org/pipermail/mitgcm-support/
+http://mailman.mitgcm.org/mailman/listinfo/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}
@@ -71,7 +76,7 @@
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
+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}
@@ -82,7 +87,6 @@
\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}
@@ -123,8 +127,8 @@
\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},
+ & 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. \\
@@ -242,7 +246,7 @@
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
+the
\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
MITgcm-support@mitgcm.org
\begin{rawhtml} </A> \end{rawhtml}
@@ -273,21 +277,21 @@
\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}.
-
+
\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
@@ -297,7 +301,7 @@
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
@@ -308,16 +312,16 @@
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{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}
@@ -362,7 +366,7 @@
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
+architectures) to the
\begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
MITgcm-support@mitgcm.org
\begin{rawhtml} </A> \end{rawhtml}
@@ -521,7 +525,6 @@
% ./mitgcmuv > output.txt
\end{verbatim}
-
\subsection{Using \texttt{genmake2}}
\label{sec:genmake}
@@ -535,13 +538,13 @@
%\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
+\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
+\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}
@@ -630,10 +633,10 @@
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
@@ -642,13 +645,13 @@
(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)
@@ -659,9 +662,9 @@
\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
+ 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
@@ -670,7 +673,7 @@
\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
@@ -679,29 +682,29 @@
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{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,
@@ -715,7 +718,6 @@
\end{description}
-
\subsection{Building with MPI}
\label{sec:mpi-build}
@@ -729,7 +731,7 @@
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{sec:genmake}. One can start with one of the examples in:
@@ -765,7 +767,7 @@
MPIexec
\begin{rawhtml} </A> \end{rawhtml}
\end{itemize}
-
+
\item Build the code with the \texttt{genmake2} \texttt{-mpi} option
(see Section \ref{sec:genmake}) using commands such as:
{\footnotesize \begin{verbatim}
@@ -773,7 +775,7 @@
% 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:
@@ -854,8 +856,6 @@
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},
@@ -865,7 +865,6 @@
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}
@@ -913,7 +912,7 @@
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
+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.
@@ -922,7 +921,7 @@
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}}.
+a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.
\subsection{Looking at the output}
@@ -977,7 +976,7 @@
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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