--- manual/s_getstarted/text/getting_started.tex	2006/06/28 17:20:51	1.38
+++ manual/s_getstarted/text/getting_started.tex	2018/01/09 01:02:48	1.47
@@ -1,37 +1,40 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.38 2006/06/28 17:20:51 molod 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}
 
-In this section, we describe how to use the model. In the first
-section, we provide enough information to help you get started with
-the model. We believe the best way to familiarize yourself with the
+We believe the best way to familiarize yourself with the
 model is to run the case study examples provided with the base
 version. Information on how to obtain, compile, and run the code is
-found there as well as a brief description of the model structure
-directory and the case study examples.  The latter and the code
-structure are described more fully in chapters
-\ref{chap:discretization} and \ref{chap:sarch}, respectively. Here, in
-this section, we provide information on how to customize the code when
-you are ready to try implementing the configuration you have in mind.
+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:
-\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}
 
 \section{Obtaining the code}
-\label{sect:obtainingCode}
+\label{sec:obtainingCode}
 \begin{rawhtml}
 <!-- CMIREDIR:obtainingCode: -->
 \end{rawhtml}
@@ -65,7 +68,7 @@
 \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
@@ -73,7 +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}
@@ -84,7 +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}
@@ -94,19 +96,23 @@
 
 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} <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}
 
@@ -121,8 +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.  \\
@@ -141,19 +147,25 @@
 the files in \texttt{CVS}!  You can also use CVS to download code
 updates.  More extensive information on using CVS for maintaining
 MITgcm code can be found
-\begin{rawhtml} <A href="http://mitgcm.org/usingcvstoget.html" target="idontexist"> \end{rawhtml}
+\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''
@@ -164,7 +176,7 @@
 \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
@@ -210,7 +222,7 @@
 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
@@ -221,11 +233,11 @@
 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:
-\begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
+\begin{rawhtml} <A href=http://mitgcm.org/download/ target="idontexist"> \end{rawhtml}
 \begin{verbatim}
 http://mitgcm.org/download/
 \end{verbatim}
@@ -234,7 +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}
@@ -265,21 +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}.
-  
+  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
@@ -289,7 +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
@@ -300,20 +312,20 @@
   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}
@@ -322,7 +334,7 @@
 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.
 
@@ -354,7 +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}
@@ -397,7 +409,7 @@
 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/* .
@@ -411,7 +423,7 @@
 
 \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
@@ -513,18 +525,31 @@
 % ./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.
 \texttt{genmake2} is a shell script written to work with all
 ``sh''--compatible shells including bash v1, bash v2, and Bourne.
-Internally, \texttt{genmake2} determines the locations of needed
-files, the compiler, compiler options, libraries, and Unix tools.  It
-relies upon a number of ``optfiles'' located in the
-\texttt{tools/build\_options} directory.
+%Internally, \texttt{genmake2} determines the locations of needed
+%files, the compiler, compiler options, libraries, and Unix tools.  It
+%relies upon a number of ``optfiles'' located in the
+%\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}
+
+\subsubsection{Optfiles in \texttt{tools/build\_options} directory:}
 
 The purpose of the optfiles is to provide all the compilation options
 for particular ``platforms'' (where ``platform'' roughly means the
@@ -597,6 +622,8 @@
 \begin{rawhtml} </A> \end{rawhtml}
 mailing list.
 
+\subsubsection{Command-line options:}
+
 In addition to the optfiles, \texttt{genmake2} supports a number of
 helpful command-line options.  A complete list of these options can be
 obtained from:
@@ -606,10 +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
@@ -618,25 +645,35 @@
   (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{--pdefault='PKG1 PKG2 PKG3 ...'}] specifies the default
-  set of packages to be used.  The normal order of precedence for
-  packages is as follows:
-  \begin{enumerate}
-  \item If available, the command line (\texttt{--pdefault}) settings
-    over-rule any others.
-
-  \item Next, \texttt{genmake2} will look for a file named
-    ``\texttt{packages.conf}'' in the local directory or in any of the
-    directories specified with the \texttt{--mods} option.
-    
-  \item Finally, if neither of the above are available,
-    \texttt{genmake2} will use the \texttt{/pkg/pkg\_default} file.
-  \end{enumerate}
-  
+
+\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)
+  \item Packages either explicitly specified or provided by default
+    (in the order given)
+  \item Packages included due to package dependencies (in the order
+    that that package dependencies are parsed)
+  \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
+  when no specific package list ({\em packages.conf})
+  is found in current directory or in any "MODS" directory.
+
 \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
@@ -645,46 +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{--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)
-  \item Packages either explicitly specified or provided by default
-    (in the order given)
-  \item Packages included due to package dependencies (in the order
-    that that package dependencies are parsed)
-  \item The "standard dirs" (which may have been specified by the
-    ``-standarddirs'' option)
-  \end{itemize}
-  
+
 \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,
@@ -698,9 +718,8 @@
 
 \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
@@ -712,12 +731,12 @@
 
 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/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">
+    href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/">
   \end{rawhtml}
   \begin{center}
     \texttt{MITgcm/tools/build\_options/}
@@ -748,15 +767,15 @@
     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:
@@ -768,14 +787,21 @@
   library and a job scheduling and queueing system such as PBS,
   LoadLeveller, Condor, or any of a number of similar tools.  A few
   example scripts (those used for our \begin{rawhtml} <A
-    href="http://mitgcm.org/testing.html"> \end{rawhtml}regular
+    href="http://mitgcm.org/public/testing.html"> \end{rawhtml}regular
   verification runs\begin{rawhtml} </A> \end{rawhtml}) are available
   at:
   \begin{rawhtml} <A
-    href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/test_scripts/">
+    href="http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example_scripts/">
+  \end{rawhtml}
+  {\footnotesize \tt
+    http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/example\_scripts/ }
+  \begin{rawhtml} </A> \end{rawhtml}
+  or at:
+  \begin{rawhtml} <A
+    href="http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/test_scripts/">
   \end{rawhtml}
   {\footnotesize \tt
-    http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }
+    http://mitgcm.org/viewvc/MITgcm/MITgcm\_contrib/test\_scripts/ }
   \begin{rawhtml} </A> \end{rawhtml}
 
 \end{enumerate}
@@ -797,12 +823,12 @@
 \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.
 
@@ -830,8 +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},
@@ -841,7 +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}
@@ -889,7 +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.
@@ -898,7 +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}
 
@@ -953,7 +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}
