--- manual/s_getstarted/text/getting_started.tex 2010/05/28 02:09:59 1.42
+++ manual/s_getstarted/text/getting_started.tex 2015/11/21 03:19:54 1.46
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.42 2010/05/28 02:09:59 jmc Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.46 2015/11/21 03:19:54 dimitri Exp $
% $Name: $
%\section{Getting started}
@@ -14,7 +14,7 @@
\ref{chap:sarch}.
\section{Where to find information}
-\label{sect:whereToFindInfo}
+\label{sec:whereToFindInfo}
\begin{rawhtml}
\end{rawhtml}
@@ -29,7 +29,7 @@
\begin{rawhtml} \end{rawhtml}
\section{Obtaining the code}
-\label{sect:obtainingCode}
+\label{sec:obtainingCode}
\begin{rawhtml}
\end{rawhtml}
@@ -63,7 +63,7 @@
\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
@@ -92,20 +92,23 @@
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} \end{rawhtml}
\begin{rawhtml} \end{rawhtml}
\begin{verbatim}
-http://mitgcm.org/source_code.html
+http://mitgcm.org/viewvc/MITgcm/MITgcm/
\end{verbatim}
\begin{rawhtml} \end{rawhtml}
@@ -142,17 +145,23 @@
MITgcm code can be found
\begin{rawhtml} \end{rawhtml}
here
-\begin{rawhtml} \end{rawhtml}
-.
+\begin{rawhtml} \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''
@@ -163,7 +172,7 @@
\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
@@ -209,7 +218,7 @@
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
@@ -220,7 +229,7 @@
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:
@@ -277,7 +286,7 @@
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)
@@ -301,7 +310,7 @@
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.
@@ -312,7 +321,7 @@
\end{itemize}
\section[Building MITgcm]{Building the code}
-\label{sect:buildingCode}
+\label{sec:buildingCode}
\begin{rawhtml}
\end{rawhtml}
@@ -321,7 +330,7 @@
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.
@@ -396,7 +405,7 @@
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/* .
@@ -410,7 +419,7 @@
\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
@@ -514,7 +523,7 @@
\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.
@@ -685,7 +694,7 @@
\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
@@ -708,7 +717,7 @@
\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
@@ -723,7 +732,7 @@
\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}
\end{rawhtml}
@@ -758,7 +767,7 @@
\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
@@ -812,12 +821,12 @@
\end{verbatim} }
\section[Running MITgcm]{Running the model in prognostic mode}
-\label{sect:runModel}
+\label{sec:runModel}
\begin{rawhtml}
\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.