--- manual/s_getstarted/text/getting_started.tex	2004/01/28 20:50:14	1.15
+++ manual/s_getstarted/text/getting_started.tex	2004/01/29 15:11:39	1.17
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.15 2004/01/28 20:50:14 edhill Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.17 2004/01/29 15:11:39 edhill Exp $
 % $Name:  $
 
 %\section{Getting started}
@@ -39,6 +39,7 @@
 \begin{rawhtml} </A> \end{rawhtml}
 Essentially all of the MITgcm web pages can be searched using a
 popular web crawler such as Google or through our own search facility:
+\begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}
 \begin{verbatim}
 http://mitgcm.org/htdig/
 \end{verbatim}
@@ -108,13 +109,13 @@
 \end{verbatim}
 or to get a specific release type:
 \begin{verbatim}
-% cvs co -d directory -P -r release1_beta1 MITgcm
+% cvs co -P -r checkpoint52i_post  MITgcm
 \end{verbatim}
 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/download'' target="idontexist"> \end{rawhtml}
 \begin{verbatim}
 http://mitgcm.org/source_code.html
 \end{verbatim}
@@ -129,7 +130,7 @@
 the files in \textit{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/usingcvstoget.html'' target="idontexist"> \end{rawhtml}
 here
 \begin{rawhtml} </A> \end{rawhtml} 
 .
@@ -149,7 +150,11 @@
 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 MITgcm-support list.
+the 
+\begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
+MITgcm-support@mitgcm.org
+\begin{rawhtml} </A> \end{rawhtml}
+mailing list.
 
 \paragraph*{Upgrading from an earlier version}
 
@@ -161,9 +166,9 @@
 \end{verbatim}
 and then issue the cvs update command such as:
 \begin{verbatim}
-% cvs -q update -r release1_beta1 -d -P
+% cvs -q update -r checkpoint52i_post -d -P
 \end{verbatim}
-This will update the ``tag'' to ``release1\_beta1'', add any new
+This will update the ``tag'' to ``checkpoint52i\_post'', add any new
 directories (-d) and remove any empty directories (-P). The -q option
 means be quiet which will reduce the number of messages you'll see in
 the terminal. If you have modified the code prior to upgrading, CVS
@@ -177,6 +182,7 @@
 cvs update command and it will report the conflicts. Conflicts are
 indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and
 ``$>>>>>>>$''. For example,
+{\small
 \begin{verbatim}
 <<<<<<< ini_parms.F
      & bottomDragLinear,myOwnBottomDragCoefficient,
@@ -184,13 +190,16 @@
      & bottomDragLinear,bottomDragQuadratic,
 >>>>>>> 1.18
 \end{verbatim}
+}
 means that you added ``myOwnBottomDragCoefficient'' to a namelist at
 the same time and place that we added ``bottomDragQuadratic''. You
 need to resolve this conflict and in this case the line should be
 changed to:
+{\small
 \begin{verbatim}
      & bottomDragLinear,bottomDragQuadratic,myOwnBottomDragCoefficient,
 \end{verbatim}
+}
 and the lines with the delimiters ($<<<<<<$,======,$>>>>>>$) be deleted.
 Unless you are making modifications which exactly parallel
 developments we make, these types of conflicts should be rare.
@@ -224,55 +233,62 @@
 \textit{eesupp} directory. The grid point model code is held under the
 \textit{model} directory. Code execution actually starts in the
 \textit{eesupp} routines and not in the \textit{model} routines. For
-this reason the top-level
-\textit{MAIN.F} is in the \textit{eesupp/src} directory. In general,
-end-users should not need to worry about this level. The top-level routine
-for the numerical part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F%
-}. Here is a brief description of the directory structure of the model under
-the root tree (a detailed description is given in section 3: Code structure).
+this reason the top-level \textit{MAIN.F} is in the
+\textit{eesupp/src} directory. In general, end-users should not need
+to worry about this level. The top-level routine for the numerical
+part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is
+a brief description of the directory structure of the model under the
+root tree (a detailed description is given in section 3: Code
+structure).
 
 \begin{itemize}
-\item \textit{bin}: this directory is initially empty. It is the default
-directory in which to compile the code.
 
+\item \textit{bin}: this directory is initially empty. It is the
+  default directory in which to compile the code.
+  
 \item \textit{diags}: contains the code relative to time-averaged
-diagnostics. It is subdivided into two subdirectories \textit{inc} and 
-\textit{src} that contain include files (*.\textit{h} files) and Fortran
-subroutines (*.\textit{F} files), respectively.
+  diagnostics. It is subdivided into two subdirectories \textit{inc}
+  and \textit{src} that contain include files (*.\textit{h} files) and
+  Fortran subroutines (*.\textit{F} files), respectively.
 
 \item \textit{doc}: contains brief documentation notes.
-
-\item \textit{eesupp}: contains the execution environment source code. Also
-subdivided into two subdirectories \textit{inc} and \textit{src}.
-
-\item \textit{exe}: this directory is initially empty. It is the default
-directory in which to execute the code.
-
-\item \textit{model}: this directory contains the main source code. Also
-subdivided into two subdirectories \textit{inc} and \textit{src}.
-
-\item \textit{pkg}: contains the source code for the packages. Each package
-corresponds to a subdirectory. For example, \textit{gmredi} contains the
-code related to the Gent-McWilliams/Redi scheme, \textit{aim} the code
-relative to the atmospheric intermediate physics. The packages are described
-in detail in section 3.
-
-\item \textit{tools}: this directory contains various useful tools. For
-example, \textit{genmake2} is a script written in csh (C-shell) that should
-be used to generate your makefile. The directory \textit{adjoint} contains
-the makefile specific to the Tangent linear and Adjoint Compiler (TAMC) that
-generates the adjoint code. The latter is described in details in part V.
-
+  
+\item \textit{eesupp}: contains the execution environment source code.
+  Also subdivided into two subdirectories \textit{inc} and
+  \textit{src}.
+  
+\item \textit{exe}: this directory is initially empty. It is the
+  default directory in which to execute the code.
+  
+\item \textit{model}: this directory contains the main source code.
+  Also subdivided into two subdirectories \textit{inc} and
+  \textit{src}.
+  
+\item \textit{pkg}: contains the source code for the packages. Each
+  package corresponds to a subdirectory. For example, \textit{gmredi}
+  contains the code related to the Gent-McWilliams/Redi scheme,
+  \textit{aim} the code relative to the atmospheric intermediate
+  physics. The packages are described in detail in section 3.
+  
+\item \textit{tools}: this directory contains various useful tools.
+  For example, \textit{genmake2} is a script written in csh (C-shell)
+  that should be used to generate your makefile. The directory
+  \textit{adjoint} contains the makefile specific to the Tangent
+  linear and Adjoint Compiler (TAMC) that generates the adjoint code.
+  The latter is described in details in part V.
+  
 \item \textit{utils}: this directory contains various utilities. The
-subdirectory \textit{knudsen2} contains code and a makefile that
-compute coefficients of the polynomial approximation to the knudsen
-formula for an ocean nonlinear equation of state. The \textit{matlab}
-subdirectory contains matlab scripts for reading model output directly
-into matlab. \textit{scripts} contains C-shell post-processing
-scripts for joining processor-based and tiled-based model output.
+  subdirectory \textit{knudsen2} contains code and a makefile that
+  compute coefficients of the polynomial approximation to the knudsen
+  formula for an ocean nonlinear equation of state. The
+  \textit{matlab} subdirectory contains matlab scripts for reading
+  model output directly into matlab. \textit{scripts} contains C-shell
+  post-processing scripts for joining processor-based and tiled-based
+  model output.
+  
+\item \textit{verification}: this directory contains the model
+  examples. See section \ref{sect:modelExamples}.
 
-\item \textit{verification}: this directory contains the model examples. See
-section \ref{sect:modelExamples}.
 \end{itemize}
 
 \section{Example experiments}
@@ -294,6 +310,7 @@
 \subsection{Full list of model examples}
 
 \begin{enumerate}
+  
 \item \textit{exp0} - single layer, ocean double gyre (barotropic with
   free-surface). This experiment is described in detail in section
   \ref{sect:eg-baro}.
@@ -383,53 +400,56 @@
 
 \begin{itemize}
 \item \textit{code}: contains the code particular to the example. At a
-minimum, this directory includes the following files:
+  minimum, this directory includes the following files:
 
-\begin{itemize}
-\item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
-  the ``execution environment'' part of the code. The default version
-  is located in \textit{eesupp/inc}.
-  
-\item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the
-  ``numerical model'' part of the code. The default version is located
-  in \textit{model/inc}.
+  \begin{itemize}
+  \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
+    the ``execution environment'' part of the code. The default
+    version is located in \textit{eesupp/inc}.
+  
+  \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
+    the ``numerical model'' part of the code. The default version is
+    located in \textit{model/inc}.
+  
+  \item \textit{code/SIZE.h}: declares size of underlying
+    computational grid.  The default version is located in
+    \textit{model/inc}.
+  \end{itemize}
+  
+  In addition, other include files and subroutines might be present in
+  \textit{code} depending on the particular experiment. See Section 2
+  for more details.
   
-\item \textit{code/SIZE.h}: declares size of underlying computational
-  grid.  The default version is located in \textit{model/inc}.
-\end{itemize}
-
-In addition, other include files and subroutines might be present in
-\textit{code} depending on the particular experiment. See Section 2
-for more details.
-
 \item \textit{input}: contains the input data files required to run
   the example. At a minimum, the \textit{input} directory contains the
   following files:
 
-\begin{itemize}
-\item \textit{input/data}: this file, written as a namelist, specifies
-  the main parameters for the experiment.
-  
-\item \textit{input/data.pkg}: contains parameters relative to the
-  packages used in the experiment.
-  
-\item \textit{input/eedata}: this file contains ``execution
-  environment'' data. At present, this consists of a specification of
-  the number of threads to use in $X$ and $Y$ under multithreaded
-  execution.
+  \begin{itemize}
+  \item \textit{input/data}: this file, written as a namelist,
+    specifies the main parameters for the experiment.
+  
+  \item \textit{input/data.pkg}: contains parameters relative to the
+    packages used in the experiment.
+  
+  \item \textit{input/eedata}: this file contains ``execution
+    environment'' data. At present, this consists of a specification
+    of the number of threads to use in $X$ and $Y$ under multithreaded
+    execution.
+  \end{itemize}
+  
+  In addition, you will also find in this directory the forcing and
+  topography files as well as the files describing the initial state
+  of the experiment.  This varies from experiment to experiment. See
+  section 2 for more details.
+
+\item \textit{results}: this directory contains the output file
+  \textit{output.txt} produced by the simulation example. This file is
+  useful for comparison with your own output when you run the
+  experiment.
 \end{itemize}
 
-In addition, you will also find in this directory the forcing and topography
-files as well as the files describing the initial state of the experiment.
-This varies from experiment to experiment. See section 2 for more details.
-
-\item \textit{results}: this directory contains the output file \textit{%
-output.txt} produced by the simulation example. This file is useful for
-comparison with your own output when you run the experiment.
-\end{itemize}
-
-Once you have chosen the example you want to run, you are ready to compile
-the code.
+Once you have chosen the example you want to run, you are ready to
+compile the code.
 
 \section{Building the code}
 \label{sect:buildingCode}
@@ -437,44 +457,67 @@
 To compile the code, we use the {\em make} program. This uses a file
 ({\em 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 ({\em genmake}), described in section
-\ref{sect:genmake}, that automatically creates the {\em Makefile} for
-you. You then need to build the dependencies and compile the code.
+dependencies. We supply a script ({\em genmake2}), described in
+section \ref{sect:genmake}, that automatically creates the {\em
+  Makefile} for you. You then need to build the dependencies and
+compile the code.
 
 As an example, let's assume that you want to build and run experiment
-\textit{verification/exp2}. The are multiple ways and places to actually
-do this but here let's build the code in
+\textit{verification/exp2}. The are multiple ways and places to
+actually do this but here let's build the code in
 \textit{verification/exp2/input}:
 \begin{verbatim}
 % cd verification/exp2/input
 \end{verbatim}
 First, build the {\em Makefile}:
 \begin{verbatim}
-% ../../../tools/genmake -mods=../code
+% ../../../tools/genmake2 -mods=../code
 \end{verbatim}
 The command line option tells {\em genmake} to override model source
 code with any files in the directory {\em ./code/}.
 
-If there is no \textit{.genmakerc} in the \textit{input} directory, you have
-to use the following options when invoking \textit{genmake}:
+On many systems, the {\em genmake2} program will be able to
+automatically recognize the hardware, find compilers and other tools
+within the user's path (``echo \$PATH''), and then choose an
+appropriate set of options from the files contained in the {\em
+  tools/build\_options} directory.  Under some circumstances, a user
+may have to create a new ``optfile'' in order to specify the exact
+combination of compiler, compiler flags, libraries, and other options
+necessary to build a particular configuration of MITgcm.  In such
+cases, it is generally helpful to read the existing ``optfiles'' and
+mimic their syntax.
+
+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}
+list.
+
+To specify an optfile to {\em genmake2}, the syntax is:
 \begin{verbatim}
-% ../../../tools/genmake  -mods=../code
+% ../../../tools/genmake2 -mods=../code -of /path/to/optfile
 \end{verbatim}
 
-Next, create the dependencies:
+Once a {\em Makefile} has been generated, we create the dependencies:
 \begin{verbatim}
 % make depend
 \end{verbatim}
-This modifies {\em Makefile} by attaching a [long] list of files on
-which other files depend. The purpose of this is to reduce
-re-compilation if and when you start to modify the code. {\tt make
-depend} also created links from the model source to this directory.
+This modifies the {\em Makefile} by attaching a [long] list of files
+upon which other files depend. The purpose of this is to reduce
+re-compilation if and when you start to modify the code. The {\tt make
+  depend} command also creates links from the model source to this
+directory.
 
-Now compile the code:
+Next compile the code:
 \begin{verbatim}
 % make
 \end{verbatim}
 The {\tt make} command creates an executable called \textit{mitgcmuv}.
+Additional make ``targets'' are defined within the makefile to aid in
+the production of adjoint and other versions of MITgcm.
 
 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 with:
@@ -492,17 +535,18 @@
 convenience. You can also configure and compile the code in other
 locations, for example on a scratch disk with out having to copy the
 entire source tree. The only requirement to do so is you have {\tt
-genmake} in your path or you know the absolute path to {\tt genmake}.
+  genmake2} in your path or you know the absolute path to {\tt
+  genmake2}.
 
-The following sections outline some possible methods of organizing you
-source and data.
+The following sections outline some possible methods of organizing
+your source and data.
 
 \subsubsection{Building from the {\em ../code directory}}
 
 This is just as simple as building in the {\em input/} directory:
 \begin{verbatim}
 % cd verification/exp2/code
-% ../../../tools/genmake
+% ../../../tools/genmake2
 % make depend
 % make
 \end{verbatim}
@@ -531,7 +575,7 @@
 % cd verification/exp2
 % mkdir build
 % cd build
-% ../../../tools/genmake -mods=../code
+% ../../../tools/genmake2 -mods=../code
 % make depend
 % make
 \end{verbatim}
@@ -553,7 +597,7 @@
 % ./mitgcmuv > output.txt
 \end{verbatim}
 
-\subsubsection{Building from on a scratch disk}
+\subsubsection{Building on a scratch disk}
 
 Model object files and output data can use up large amounts of disk
 space so it is often the case that you will be operating on a large
@@ -561,7 +605,8 @@
 following commands will build the model in {\em /scratch/exp2-run1}:
 \begin{verbatim}
 % cd /scratch/exp2-run1
-% ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
+% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
+  -mods=~/MITgcm/verification/exp2/code
 % make depend
 % make
 \end{verbatim}
@@ -577,7 +622,8 @@
 % cd /scratch/exp2
 % mkdir build
 % cd build
-% ~/MITgcm/tools/genmake -rootdir=~/MITgcm -mods=~/MITgcm/verification/exp2/code
+% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
+  -mods=~/MITgcm/verification/exp2/code
 % make depend
 % make
 % cd ../
@@ -588,107 +634,166 @@
 
 
 
-\subsection{\textit{genmake}}
+\subsection{Using \textit{genmake2}}
 \label{sect:genmake}
 
-To compile the code, use the script \textit{genmake} located in the \textit{%
-tools} directory. \textit{genmake} is a script that generates the makefile.
-It has been written so that the code can be compiled on a wide diversity of
-machines and systems. However, if it doesn't work the first time on your
-platform, you might need to edit certain lines of \textit{genmake} in the
-section containing the setups for the different machines. The file is
-structured like this:
-\begin{verbatim}
-        .
-        .
-        .
-general instructions (machine independent)
-        .
-        .
-        .
-    - setup machine 1
-    - setup machine 2
-    - setup machine 3
-    - setup machine 4
-       etc
-        .
-        .
-        .
-\end{verbatim}
-
-For example, the setup corresponding to a DEC alpha machine is reproduced
-here:
-\begin{verbatim}
-  case OSF1+mpi:
-    echo "Configuring for DEC Alpha"
-    set CPP        = ( '/usr/bin/cpp -P' )
-    set DEFINES    = ( ${DEFINES}  '-DTARGET_DEC -DWORDLENGTH=1' )
-    set KPP        = ( 'kapf' )
-    set KPPFILES   = ( 'main.F' )
-    set KFLAGS1    = ( '-scan=132 -noconc -cmp=' )
-    set FC         = ( 'f77' )
-    set FFLAGS     = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' )
-    set FOPTIM     = ( '-O5 -fast -tune host -inline all' )
-    set NOOPTFLAGS = ( '-O0' )
-    set LIBS       = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' )
-    set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')
-    set RMFILES    = ( '*.p.out' )
-    breaksw
-\end{verbatim}
-
-Typically, these are the lines that you might need to edit to make \textit{%
-genmake} work on your platform if it doesn't work the first time. \textit{%
-genmake} understands several options that are described here:
-
-\begin{itemize}
-\item -rootdir=dir
-
-indicates where the model root directory is relative to the directory where
-you are compiling. This option is not needed if you compile in the \textit{%
-bin} directory (which is the default compilation directory) or within the 
-\textit{verification} tree.
-
-\item -mods=dir1,dir2,...
-
-indicates the relative or absolute paths directories where the sources
-should take precedence over the default versions (located in \textit{model}, 
-\textit{eesupp},...). Typically, this option is used when running the
-examples, see below.
-
-\item -enable=pkg1,pkg2,...
-
-enables packages source code \textit{pkg1}, \textit{pkg2},... when creating
-the makefile.
-
-\item -disable=pkg1,pkg2,...
-
-disables packages source code \textit{pkg1}, \textit{pkg2},... when creating
-the makefile.
+To compile the code, first use the program \texttt{genmake2} (located
+in the \textit{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 {\em
+  tools/build\_options} directory.
+
+The purpose of the optfiles is to provide all the compilation options
+for particular ``platforms'' (where ``platform'' roughly means the
+combination of the hardware and the compiler) and code configurations.
+Given the combinations of possible compilers and library dependencies
+({\it eg.}  MPI and NetCDF) there may be numerous optfiles available
+for a single machine.  The naming scheme for the majority of the
+optfiles shipped with the code is
+\begin{center}
+  {\bf OS\_HARDWARE\_COMPILER }
+\end{center}
+where
+\begin{description}
+\item[OS] is the name of the operating system (generally the
+  lower-case output of the {\tt 'uname'} command)
+\item[HARDWARE] is a string that describes the CPU type and
+  corresponds to output from the  {\tt 'uname -m'} command:
+  \begin{description}
+  \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
+    and athlon
+  \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
+  \item[amd64] is AMD x86\_64 systems
+  \item[ppc] is for Mac PowerPC systems
+  \end{description}
+\item[COMPILER] is the compiler name (generally, the name of the
+  FORTRAN executable)
+\end{description}
 
-\item -platform=machine
+In many cases, the default optfiles are sufficient and will result in
+usable Makefiles.  However, for some machines or code configurations,
+new ``optfiles'' must be written. To create a new optfile, it is
+generally best to start with one of the defaults and modify it to suit
+your needs.  Like \texttt{genmake2}, the optfiles are all written
+using a simple ``sh''--compatible syntax.  While nearly all variables
+used within \texttt{genmake2} may be specified in the optfiles, the
+critical ones that should be defined are:
 
-specifies the platform for which you want the makefile. In general, you
-won't need this option. \textit{genmake} will select the right machine for
-you (the one you're working on!). However, this option is useful if you have
-a choice of several compilers on one machine and you want to use the one
-that is not the default (ex: \texttt{pgf77} instead of \texttt{f77} under
-Linux).
+\begin{description}
+\item[FC] the FORTRAN compiler (executable) to use
+\item[DEFINES] the command-line DEFINE options passed to the compiler
+\item[CPP] the C pre-processor to use
+\item[NOOPTFLAGS] options flags for special files that should not be
+  optimized
+\end{description}
 
-\item -mpi
+For example, the optfile for a typical Red Hat Linux machine (``ia32''
+architecture) using the GCC (g77) compiler is
+\begin{verbatim}
+FC=g77
+DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
+CPP='cpp  -traditional -P'
+NOOPTFLAGS='-O0'
+#  For IEEE, use the "-ffloat-store" option
+if test "x$IEEE" = x ; then
+    FFLAGS='-Wimplicit -Wunused -Wuninitialized'
+    FOPTIM='-O3 -malign-double -funroll-loops'
+else
+    FFLAGS='-Wimplicit -Wunused -ffloat-store'
+    FOPTIM='-O0 -malign-double'
+fi
+\end{verbatim}
+
+If you write an optfile for an unrepresented machine or compiler, you
+are strongly encouraged to submit the optfile to the MITgcm project
+for inclusion.  Please send the file to the
+\begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
+\begin{center}
+  MITgcm-support@mitgcm.org
+\end{center}
+\begin{rawhtml} </A> \end{rawhtml}
+mailing list.
 
-this is used when you want to run the model in parallel processing mode
-under mpi (see section on parallel computation for more details).
+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:
+\begin{verbatim}
+% genmake2 -h
+\end{verbatim}
 
-\item -jam
+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
+    tools/build\_options}.  The method used for making this guess is
+  to first determine the combination of operating system and hardware
+  (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{--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
+  "PKGNAME1 (+|-)PKGNAME2" pairwise rule where the "+" or "-" symbol
+  specifies a "must be used with" or a "must not be used with"
+  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{--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}
+  
+\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{--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.
 
-this is used when you want to run the model in parallel processing mode
-under jam (see section on parallel computation for more details).
-\end{itemize}
+\end{description}
 
-For some of the examples, there is a file called \textit{.genmakerc} in the 
-\textit{input} directory that has the relevant \textit{genmake} options for
-that particular example. In this way you don't need to type the options when
-invoking \textit{genmake}.
 
 
 \section{Running the model}
@@ -714,7 +819,7 @@
 % ./mitgcmuv > output.txt
 \end{verbatim}
 
-For the example experiments in {\em vericication}, an example of the
+For the example experiments in {\em verification}, an example of the
 output is kept in {\em results/output.txt} for comparison. You can compare
 your {\em output.txt} with this one to check that the set-up works.
 
@@ -803,123 +908,128 @@
 \section{Doing it yourself: customizing the code}
 
 When you are ready to run the model in the configuration you want, the
-easiest thing is to use and adapt the setup of the case studies experiment
-(described previously) that is the closest to your configuration. Then, the
-amount of setup will be minimized. In this section, we focus on the setup
-relative to the ''numerical model'' part of the code (the setup relative to
-the ''execution environment'' part is covered in the parallel implementation
-section) and on the variables and parameters that you are likely to change.
+easiest thing is to use and adapt the setup of the case studies
+experiment (described previously) that is the closest to your
+configuration. Then, the amount of setup will be minimized. In this
+section, we focus on the setup relative to the ``numerical model''
+part of the code (the setup relative to the ``execution environment''
+part is covered in the parallel implementation section) and on the
+variables and parameters that you are likely to change.
 
 \subsection{Configuration and setup}
 
-The CPP keys relative to the ''numerical model'' part of the code are all
-defined and set in the file \textit{CPP\_OPTIONS.h }in the directory \textit{%
-model/inc }or in one of the \textit{code }directories of the case study
-experiments under \textit{verification.} The model parameters are defined
-and declared in the file \textit{model/inc/PARAMS.h }and their default
-values are set in the routine \textit{model/src/set\_defaults.F. }The
-default values can be modified in the namelist file \textit{data }which
-needs to be located in the directory where you will run the model. The
-parameters are initialized in the routine \textit{model/src/ini\_parms.F}.
-Look at this routine to see in what part of the namelist the parameters are
-located.
-
-In what follows the parameters are grouped into categories related to the
-computational domain, the equations solved in the model, and the simulation
-controls.
+The CPP keys relative to the ``numerical model'' part of the code are
+all defined and set in the file \textit{CPP\_OPTIONS.h }in the
+directory \textit{ model/inc }or in one of the \textit{code
+}directories of the case study experiments under
+\textit{verification.} The model parameters are defined and declared
+in the file \textit{model/inc/PARAMS.h }and their default values are
+set in the routine \textit{model/src/set\_defaults.F. }The default
+values can be modified in the namelist file \textit{data }which needs
+to be located in the directory where you will run the model. The
+parameters are initialized in the routine
+\textit{model/src/ini\_parms.F}.  Look at this routine to see in what
+part of the namelist the parameters are located.
+
+In what follows the parameters are grouped into categories related to
+the computational domain, the equations solved in the model, and the
+simulation controls.
 
 \subsection{Computational domain, geometry and time-discretization}
 
-\begin{itemize}
-\item dimensions
-\end{itemize}
-
-The number of points in the x, y,\textit{\ }and r\textit{\ }directions are
-represented by the variables \textbf{sNx}\textit{, }\textbf{sNy}\textit{, }%
-and \textbf{Nr}\textit{\ }respectively which are declared and set in the
-file \textit{model/inc/SIZE.h. }(Again, this assumes a mono-processor
-calculation. For multiprocessor calculations see section on parallel
-implementation.)
-
-\begin{itemize}
-\item grid
-\end{itemize}
-
-Three different grids are available: cartesian, spherical polar, and
-curvilinear (including the cubed sphere). The grid is set through the
-logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{%
-usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{%
-usingCurvilinearGrid}\textit{. }In the case of spherical and curvilinear
-grids, the southern boundary is defined through the variable \textbf{phiMin}%
-\textit{\ }which corresponds to the latitude of the southern most cell face
-(in degrees). The resolution along the x and y directions is controlled by
-the 1D arrays \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters
-in the case of a cartesian grid, in degrees otherwise). The vertical grid
-spacing is set through the 1D array \textbf{delz }for the ocean (in meters)
-or \textbf{delp}\textit{\ }for the atmosphere (in Pa). The variable \textbf{%
-Ro\_SeaLevel} represents the standard position of Sea-Level in ''R''
-coordinate. This is typically set to 0m for the ocean (default value) and 10$%
-^{5}$Pa for the atmosphere. For the atmosphere, also set the logical
-variable \textbf{groundAtK1} to '.\texttt{TRUE}.'. which put the first level
-(k=1) at the lower boundary (ground).
-
-For the cartesian grid case, the Coriolis parameter $f$ is set through the
-variables \textbf{f0}\textit{\ }and \textbf{beta}\textit{\ }which correspond
-to the reference Coriolis parameter (in s$^{-1}$) and $\frac{\partial f}{%
-\partial y}$(in m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ }%
-is set to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
-southern edge of the domain.
-
-\begin{itemize}
-\item topography - full and partial cells
-\end{itemize}
-
-The domain bathymetry is read from a file that contains a 2D (x,y) map of
-depths (in m) for the ocean or pressures (in Pa) for the atmosphere. The
-file name is represented by the variable \textbf{bathyFile}\textit{. }The
-file is assumed to contain binary numbers giving the depth (pressure) of the
-model at each grid cell, ordered with the x coordinate varying fastest. The
-points are ordered from low coordinate to high coordinate for both axes. The
-model code applies without modification to enclosed, periodic, and double
-periodic domains. Periodicity is assumed by default and is suppressed by
-setting the depths to 0m for the cells at the limits of the computational
-domain (note: not sure this is the case for the atmosphere). The precision
-with which to read the binary data is controlled by the integer variable 
-\textbf{readBinaryPrec }which can take the value \texttt{32} (single
-precision) or \texttt{64} (double precision). See the matlab program \textit{%
-gendata.m }in the \textit{input }directories under \textit{verification }to
-see how the bathymetry files are generated for the case study experiments.
-
-To use the partial cell capability, the variable \textbf{hFacMin}\textit{\ }%
-needs to be set to a value between 0 and 1 (it is set to 1 by default)
-corresponding to the minimum fractional size of the cell. For example if the
-bottom cell is 500m thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the
-actual thickness of the cell (i.e. used in the code) can cover a range of
-discrete values 50m apart from 50m to 500m depending on the value of the
-bottom depth (in \textbf{bathyFile}) at this point.
-
-Note that the bottom depths (or pressures) need not coincide with the models
-levels as deduced from \textbf{delz}\textit{\ }or\textit{\ }\textbf{delp}%
-\textit{. }The model will interpolate the numbers in \textbf{bathyFile}%
-\textit{\ }so that they match the levels obtained from \textbf{delz}\textit{%
-\ }or\textit{\ }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
-
-(Note: the atmospheric case is a bit more complicated than what is written
-here I think. To come soon...)
+\begin{description}
+\item[dimensions] \ 
+  
+  The number of points in the x, y,\textit{\ }and r\textit{\ 
+  }directions are represented by the variables \textbf{sNx}\textit{,
+  }\textbf{sNy}\textit{, } and \textbf{Nr}\textit{\ }respectively
+  which are declared and set in the file \textit{model/inc/SIZE.h.
+  }(Again, this assumes a mono-processor calculation. For
+  multiprocessor calculations see section on parallel implementation.)
+
+\item[grid] \ 
+  
+  Three different grids are available: cartesian, spherical polar, and
+  curvilinear (including the cubed sphere). The grid is set through
+  the logical variables \textbf{usingCartesianGrid}\textit{, }\textbf{
+    usingSphericalPolarGrid}\textit{, }and \textit{\ }\textbf{
+    usingCurvilinearGrid}\textit{. }In the case of spherical and
+  curvilinear grids, the southern boundary is defined through the
+  variable \textbf{phiMin} \textit{\ }which corresponds to the
+  latitude of the southern most cell face (in degrees). The resolution
+  along the x and y directions is controlled by the 1D arrays
+  \textbf{delx}\textit{\ }and \textbf{dely}\textit{\ }(in meters in
+  the case of a cartesian grid, in degrees otherwise). The vertical
+  grid spacing is set through the 1D array \textbf{delz }for the ocean
+  (in meters) or \textbf{delp}\textit{\ }for the atmosphere (in Pa).
+  The variable \textbf{ Ro\_SeaLevel} represents the standard position
+  of Sea-Level in ''R'' coordinate. This is typically set to 0m for
+  the ocean (default value) and 10$ ^{5}$Pa for the atmosphere. For
+  the atmosphere, also set the logical variable \textbf{groundAtK1} to
+  '.\texttt{TRUE}.'. which put the first level (k=1) at the lower
+  boundary (ground).
+  
+  For the cartesian grid case, the Coriolis parameter $f$ is set
+  through the variables \textbf{f0}\textit{\ }and
+  \textbf{beta}\textit{\ }which correspond to the reference Coriolis
+  parameter (in s$^{-1}$) and $\frac{\partial f}{ \partial y}$(in
+  m$^{-1}$s$^{-1}$) respectively. If \textbf{beta }\textit{\ } is set
+  to a nonzero value, \textbf{f0}\textit{\ }is the value of $f$ at the
+  southern edge of the domain.
+
+\item[topography - full and partial cells] \ 
+  
+  The domain bathymetry is read from a file that contains a 2D (x,y)
+  map of depths (in m) for the ocean or pressures (in Pa) for the
+  atmosphere. The file name is represented by the variable
+  \textbf{bathyFile}\textit{. }The file is assumed to contain binary
+  numbers giving the depth (pressure) of the model at each grid cell,
+  ordered with the x coordinate varying fastest. The points are
+  ordered from low coordinate to high coordinate for both axes. The
+  model code applies without modification to enclosed, periodic, and
+  double periodic domains. Periodicity is assumed by default and is
+  suppressed by setting the depths to 0m for the cells at the limits
+  of the computational domain (note: not sure this is the case for the
+  atmosphere). The precision with which to read the binary data is
+  controlled by the integer variable \textbf{readBinaryPrec }which can
+  take the value \texttt{32} (single precision) or \texttt{64} (double
+  precision). See the matlab program \textit{ gendata.m }in the
+  \textit{input }directories under \textit{verification }to see how
+  the bathymetry files are generated for the case study experiments.
+  
+  To use the partial cell capability, the variable
+  \textbf{hFacMin}\textit{\ } needs to be set to a value between 0 and
+  1 (it is set to 1 by default) corresponding to the minimum
+  fractional size of the cell. For example if the bottom cell is 500m
+  thick and \textbf{hFacMin}\textit{\ }is set to 0.1, the actual
+  thickness of the cell (i.e. used in the code) can cover a range of
+  discrete values 50m apart from 50m to 500m depending on the value of
+  the bottom depth (in \textbf{bathyFile}) at this point.
+  
+  Note that the bottom depths (or pressures) need not coincide with
+  the models levels as deduced from \textbf{delz}\textit{\ 
+  }or\textit{\ }\textbf{delp} \textit{. }The model will interpolate
+  the numbers in \textbf{bathyFile} \textit{\ }so that they match the
+  levels obtained from \textbf{delz}\textit{ \ }or\textit{\ 
+  }\textbf{delp}\textit{\ }and \textbf{hFacMin}\textit{. }
+  
+  (Note: the atmospheric case is a bit more complicated than what is
+  written here I think. To come soon...)
+
+\item[time-discretization] \ 
+  
+  The time steps are set through the real variables \textbf{deltaTMom}
+  and \textbf{deltaTtracer} (in s) which represent the time step for
+  the momentum and tracer equations, respectively. For synchronous
+  integrations, simply set the two variables to the same value (or you
+  can prescribe one time step only through the variable
+  \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
+  through the variable \textbf{abEps} (dimensionless). The stagger
+  baroclinic time stepping can be activated by setting the logical
+  variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
 
-\begin{itemize}
-\item time-discretization
-\end{itemize}
+\end{description}
 
-The time steps are set through the real variables \textbf{deltaTMom}
-and \textbf{deltaTtracer} (in s) which represent the time step for the
-momentum and tracer equations, respectively. For synchronous
-integrations, simply set the two variables to the same value (or you
-can prescribe one time step only through the variable
-\textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set
-through the variable \textbf{abEps} (dimensionless). The stagger
-baroclinic time stepping can be activated by setting the logical
-variable \textbf{staggerTimeStep} to '.\texttt{TRUE}.'.
 
 \subsection{Equation of state}
 
@@ -991,94 +1101,96 @@
 Look at the file \textit{model/inc/PARAMS.h }for a precise definition of
 these variables.
 
-\begin{itemize}
-\item initialization
-\end{itemize}
-
-The velocity components are initialized to 0 unless the simulation is
-starting from a pickup file (see section on simulation control parameters).
-
-\begin{itemize}
-\item forcing
-\end{itemize}
-
-This section only applies to the ocean. You need to generate wind-stress
-data into two files \textbf{zonalWindFile}\textit{\ }and \textbf{%
-meridWindFile }corresponding to the zonal and meridional components of the
-wind stress, respectively (if you want the stress to be along the direction
-of only one of the model horizontal axes, you only need to generate one
-file). The format of the files is similar to the bathymetry file. The zonal
-(meridional) stress data are assumed to be in Pa and located at U-points
-(V-points). As for the bathymetry, the precision with which to read the
-binary data is controlled by the variable \textbf{readBinaryPrec}.\textbf{\ }
-See the matlab program \textit{gendata.m }in the \textit{input }directories
-under \textit{verification }to see how simple analytical wind forcing data
-are generated for the case study experiments. 
-
-There is also the possibility of prescribing time-dependent periodic
-forcing. To do this, concatenate the successive time records into a single
-file (for each stress component) ordered in a (x, y, t) fashion and set the
-following variables: \textbf{periodicExternalForcing }to '.\texttt{TRUE}.', 
-\textbf{externForcingPeriod }to the period (in s) of which the forcing
-varies (typically 1 month), and \textbf{externForcingCycle }to the repeat
-time (in s) of the forcing (typically 1 year -- note: \textbf{%
-externForcingCycle }must be a multiple of \textbf{externForcingPeriod}).
-With these variables set up, the model will interpolate the forcing linearly
-at each iteration.
-
-\begin{itemize}
-\item dissipation
-\end{itemize}
-
-The lateral eddy viscosity coefficient is specified through the variable 
-\textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The vertical eddy viscosity
-coefficient is specified through the variable \textbf{viscAz }(in m$^{2}$s$%
-^{-1}$) for the ocean and \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$)
-for the atmosphere. The vertical diffusive fluxes can be computed implicitly
-by setting the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}%
-.'. In addition, biharmonic mixing can be added as well through the variable 
-\textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a spherical polar grid,
-you might also need to set the variable \textbf{cosPower} which is set to 0
-by default and which represents the power of cosine of latitude to multiply
-viscosity. Slip or no-slip conditions at lateral and bottom boundaries are
-specified through the logical variables \textbf{no\_slip\_sides}\textit{\ }%
-and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}', free-slip
-boundary conditions are applied. If no-slip boundary conditions are applied
-at the bottom, a bottom drag can be applied as well. Two forms are
-available: linear (set the variable \textbf{bottomDragLinear}\textit{\ }in s$%
-^{-1}$) and quadratic (set the variable \textbf{bottomDragQuadratic}\textit{%
-\ }in m$^{-1}$).
-
-The Fourier and Shapiro filters are described elsewhere.
-
-\begin{itemize}
-\item C-D scheme
-\end{itemize}
+\begin{description}
+\item[initialization] \ 
+  
+  The velocity components are initialized to 0 unless the simulation
+  is starting from a pickup file (see section on simulation control
+  parameters).
+
+\item[forcing] \ 
+  
+  This section only applies to the ocean. You need to generate
+  wind-stress data into two files \textbf{zonalWindFile}\textit{\ }and
+  \textbf{ meridWindFile }corresponding to the zonal and meridional
+  components of the wind stress, respectively (if you want the stress
+  to be along the direction of only one of the model horizontal axes,
+  you only need to generate one file). The format of the files is
+  similar to the bathymetry file. The zonal (meridional) stress data
+  are assumed to be in Pa and located at U-points (V-points). As for
+  the bathymetry, the precision with which to read the binary data is
+  controlled by the variable \textbf{readBinaryPrec}.\textbf{\ } See
+  the matlab program \textit{gendata.m }in the \textit{input
+  }directories under \textit{verification }to see how simple
+  analytical wind forcing data are generated for the case study
+  experiments.
+  
+  There is also the possibility of prescribing time-dependent periodic
+  forcing. To do this, concatenate the successive time records into a
+  single file (for each stress component) ordered in a (x, y, t)
+  fashion and set the following variables:
+  \textbf{periodicExternalForcing }to '.\texttt{TRUE}.',
+  \textbf{externForcingPeriod }to the period (in s) of which the
+  forcing varies (typically 1 month), and \textbf{externForcingCycle
+  }to the repeat time (in s) of the forcing (typically 1 year -- note:
+  \textbf{ externForcingCycle }must be a multiple of
+  \textbf{externForcingPeriod}).  With these variables set up, the
+  model will interpolate the forcing linearly at each iteration.
+
+\item[dissipation] \ 
+  
+  The lateral eddy viscosity coefficient is specified through the
+  variable \textbf{viscAh}\textit{\ }(in m$^{2}$s$^{-1}$). The
+  vertical eddy viscosity coefficient is specified through the
+  variable \textbf{viscAz }(in m$^{2}$s$ ^{-1}$) for the ocean and
+  \textbf{viscAp}\textit{\ }(in Pa$^{2}$s$^{-1}$) for the atmosphere.
+  The vertical diffusive fluxes can be computed implicitly by setting
+  the logical variable \textbf{implicitViscosity }to '.\texttt{TRUE}
+  .'. In addition, biharmonic mixing can be added as well through the
+  variable \textbf{viscA4}\textit{\ }(in m$^{4}$s$^{-1}$). On a
+  spherical polar grid, you might also need to set the variable
+  \textbf{cosPower} which is set to 0 by default and which represents
+  the power of cosine of latitude to multiply viscosity. Slip or
+  no-slip conditions at lateral and bottom boundaries are specified
+  through the logical variables \textbf{no\_slip\_sides}\textit{\ }
+  and \textbf{no\_slip\_bottom}. If set to '\texttt{.FALSE.}',
+  free-slip boundary conditions are applied. If no-slip boundary
+  conditions are applied at the bottom, a bottom drag can be applied
+  as well. Two forms are available: linear (set the variable
+  \textbf{bottomDragLinear}\textit{\ }in s$ ^{-1}$) and quadratic (set
+  the variable \textbf{bottomDragQuadratic}\textit{ \ }in m$^{-1}$).
+
+  The Fourier and Shapiro filters are described elsewhere.
+
+\item[C-D scheme] \ 
+  
+  If you run at a sufficiently coarse resolution, you will need the
+  C-D scheme for the computation of the Coriolis terms. The
+  variable\textbf{\ tauCD}, which represents the C-D scheme coupling
+  timescale (in s) needs to be set.
+  
+\item[calculation of pressure/geopotential] \ 
+  
+  First, to run a non-hydrostatic ocean simulation, set the logical
+  variable \textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure
+  field is then inverted through a 3D elliptic equation. (Note: this
+  capability is not available for the atmosphere yet.) By default, a
+  hydrostatic simulation is assumed and a 2D elliptic equation is used
+  to invert the pressure field. The parameters controlling the
+  behaviour of the elliptic solvers are the variables
+  \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual } for
+  the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{
+    cg3dTargetResidual }for the 3D case. You probably won't need to
+  alter the default values (are we sure of this?).
+  
+  For the calculation of the surface pressure (for the ocean) or
+  surface geopotential (for the atmosphere) you need to set the
+  logical variables \textbf{rigidLid} and
+  \textbf{implicitFreeSurface}\textit{\ }(set one to '.
+  \texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how
+  you want to deal with the ocean upper or atmosphere lower boundary).
 
-If you run at a sufficiently coarse resolution, you will need the C-D scheme
-for the computation of the Coriolis terms. The variable\textbf{\ tauCD},
-which represents the C-D scheme coupling timescale (in s) needs to be set.
-
-\begin{itemize} 
-\item calculation of pressure/geopotential
-\end{itemize} 
-
-First, to run a non-hydrostatic ocean simulation, set the logical variable 
-\textbf{nonHydrostatic} to '.\texttt{TRUE}.'. The pressure field is then
-inverted through a 3D elliptic equation. (Note: this capability is not
-available for the atmosphere yet.) By default, a hydrostatic simulation is
-assumed and a 2D elliptic equation is used to invert the pressure field. The
-parameters controlling the behaviour of the elliptic solvers are the
-variables \textbf{cg2dMaxIters}\textit{\ }and \textbf{cg2dTargetResidual }%
-for the 2D case and \textbf{cg3dMaxIters}\textit{\ }and \textbf{%
-cg3dTargetResidual }for the 3D case. You probably won't need to alter the
-default values (are we sure of this?).
-
-For the calculation of the surface pressure (for the ocean) or surface
-geopotential (for the atmosphere) you need to set the logical variables 
-\textbf{rigidLid} and \textbf{implicitFreeSurface}\textit{\ }(set one to '.%
-\texttt{TRUE}.' and the other to '.\texttt{FALSE}.' depending on how you
-want to deal with the ocean upper or atmosphere lower boundary).
+\end{description} 
 
 \subsection{Tracer equations}
 
@@ -1086,90 +1198,92 @@
 equation and the salinity (for the ocean) or specific humidity (for the
 atmosphere) equation. As for the momentum equations, we only describe for
 now the parameters that you are likely to change. The logical variables 
-\textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{%
+\textbf{tempDiffusion}\textit{, }\textbf{tempAdvection}\textit{, }\textbf{
 tempForcing}\textit{,} and \textbf{tempStepping} allow you to turn on/off
 terms in the temperature equation (same thing for salinity or specific
-humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{%
+humidity with variables \textbf{saltDiffusion}\textit{, }\textbf{
 saltAdvection}\textit{\ }etc). These variables are all assumed here to be
 set to '.\texttt{TRUE}.'. Look at file \textit{model/inc/PARAMS.h }for a
 precise definition.
 
-\begin{itemize}
-\item initialization
-\end{itemize}
-
-The initial tracer data can be contained in the binary files \textbf{%
-hydrogThetaFile }and \textbf{hydrogSaltFile}. These files should contain 3D
-data ordered in an (x, y, r) fashion with k=1 as the first vertical level.
-If no file names are provided, the tracers are then initialized with the
-values of \textbf{tRef }and \textbf{sRef }mentioned above (in the equation
-of state section). In this case, the initial tracer data are uniform in x
-and y for each depth level.
-
-\begin{itemize} 
-\item forcing
-\end{itemize}
-
-This part is more relevant for the ocean, the procedure for the atmosphere
-not being completely stabilized at the moment.
-
-A combination of fluxes data and relaxation terms can be used for driving
-the tracer equations. \ For potential temperature, heat flux data (in W/m$%
-^{2}$) can be stored in the 2D binary file \textbf{surfQfile}\textit{. }%
-Alternatively or in addition, the forcing can be specified through a
-relaxation term. The SST data to which the model surface temperatures are
-restored to are supposed to be stored in the 2D binary file \textbf{%
-thetaClimFile}\textit{. }The corresponding relaxation time scale coefficient
-is set through the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The
-same procedure applies for salinity with the variable names \textbf{EmPmRfile%
-}\textit{, }\textbf{saltClimFile}\textit{, }and \textbf{tauSaltClimRelax}%
-\textit{\ }for freshwater flux (in m/s) and surface salinity (in ppt) data
-files and relaxation time scale coefficient (in s), respectively. Also for
-salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on, natural
-boundary conditions are applied i.e. when computing the surface salinity
-tendency, the freshwater flux is multiplied by the model surface salinity
-instead of a constant salinity value.
-
-As for the other input files, the precision with which to read the data is
-controlled by the variable \textbf{readBinaryPrec}. Time-dependent, periodic
-forcing can be applied as well following the same procedure used for the
-wind forcing data (see above).
-
-\begin{itemize}
-\item dissipation
-\end{itemize}
-
-Lateral eddy diffusivities for temperature and salinity/specific humidity
-are specified through the variables \textbf{diffKhT }and \textbf{diffKhS }%
-(in m$^{2}$/s). Vertical eddy diffusivities are specified through the
-variables \textbf{diffKzT }and \textbf{diffKzS }(in m$^{2}$/s) for the ocean
-and \textbf{diffKpT }and \textbf{diffKpS }(in Pa$^{2}$/s) for the
-atmosphere. The vertical diffusive fluxes can be computed implicitly by
-setting the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
-.'. In addition, biharmonic diffusivities can be specified as well through
-the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in m$^{4}$/s). Note
-that the cosine power scaling (specified through \textbf{cosPower }- see the
-momentum equations section) is applied to the tracer diffusivities
-(Laplacian and biharmonic) as well. The Gent and McWilliams parameterization
-for oceanic tracers is described in the package section. Finally, note that
-tracers can be also subject to Fourier and Shapiro filtering (see the
-corresponding section on these filters).
-
-\begin{itemize}
-\item ocean convection
-\end{itemize}
+\begin{description}
+\item[initialization] \ 
+  
+  The initial tracer data can be contained in the binary files
+  \textbf{ hydrogThetaFile }and \textbf{hydrogSaltFile}. These files
+  should contain 3D data ordered in an (x, y, r) fashion with k=1 as
+  the first vertical level.  If no file names are provided, the
+  tracers are then initialized with the values of \textbf{tRef }and
+  \textbf{sRef }mentioned above (in the equation of state section). In
+  this case, the initial tracer data are uniform in x and y for each
+  depth level.
+
+\item[forcing] \ 
+  
+  This part is more relevant for the ocean, the procedure for the
+  atmosphere not being completely stabilized at the moment.
+  
+  A combination of fluxes data and relaxation terms can be used for
+  driving the tracer equations. \ For potential temperature, heat flux
+  data (in W/m$ ^{2}$) can be stored in the 2D binary file
+  \textbf{surfQfile}\textit{. }  Alternatively or in addition, the
+  forcing can be specified through a relaxation term. The SST data to
+  which the model surface temperatures are restored to are supposed to
+  be stored in the 2D binary file \textbf{ thetaClimFile}\textit{.
+  }The corresponding relaxation time scale coefficient is set through
+  the variable \textbf{tauThetaClimRelax}\textit{\ }(in s). The same
+  procedure applies for salinity with the variable names
+  \textbf{EmPmRfile }\textit{, }\textbf{saltClimFile}\textit{, }and
+  \textbf{tauSaltClimRelax} \textit{\ }for freshwater flux (in m/s)
+  and surface salinity (in ppt) data files and relaxation time scale
+  coefficient (in s), respectively. Also for salinity, if the CPP key
+  \textbf{USE\_NATURAL\_BCS} is turned on, natural boundary conditions
+  are applied i.e. when computing the surface salinity tendency, the
+  freshwater flux is multiplied by the model surface salinity instead
+  of a constant salinity value.
+  
+  As for the other input files, the precision with which to read the
+  data is controlled by the variable \textbf{readBinaryPrec}.
+  Time-dependent, periodic forcing can be applied as well following
+  the same procedure used for the wind forcing data (see above).
+
+\item[dissipation] \ 
+  
+  Lateral eddy diffusivities for temperature and salinity/specific
+  humidity are specified through the variables \textbf{diffKhT }and
+  \textbf{diffKhS } (in m$^{2}$/s). Vertical eddy diffusivities are
+  specified through the variables \textbf{diffKzT }and \textbf{diffKzS
+  }(in m$^{2}$/s) for the ocean and \textbf{diffKpT }and
+  \textbf{diffKpS }(in Pa$^{2}$/s) for the atmosphere. The vertical
+  diffusive fluxes can be computed implicitly by setting the logical
+  variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'. In
+  addition, biharmonic diffusivities can be specified as well through
+  the coefficients \textbf{diffK4T }and \textbf{diffK4S }(in
+  m$^{4}$/s). Note that the cosine power scaling (specified through
+  \textbf{cosPower }- see the momentum equations section) is applied
+  to the tracer diffusivities (Laplacian and biharmonic) as well. The
+  Gent and McWilliams parameterization for oceanic tracers is
+  described in the package section. Finally, note that tracers can be
+  also subject to Fourier and Shapiro filtering (see the corresponding
+  section on these filters).
+
+\item[ocean convection] \ 
+  
+  Two options are available to parameterize ocean convection: one is
+  to use the convective adjustment scheme. In this case, you need to
+  set the variable \textbf{cadjFreq}, which represents the frequency
+  (in s) with which the adjustment algorithm is called, to a non-zero
+  value (if set to a negative value by the user, the model will set it
+  to the tracer time step). The other option is to parameterize
+  convection with implicit vertical diffusion. To do this, set the
+  logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE} .'
+  and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s)
+  you wish the tracer vertical diffusivities to have when mixing
+  tracers vertically due to static instabilities. Note that
+  \textbf{cadjFreq }and \textbf{ivdc\_kappa }can not both have
+  non-zero value.
 
-Two options are available to parameterize ocean convection: one is to use
-the convective adjustment scheme. In this case, you need to set the variable 
-\textbf{cadjFreq}, which represents the frequency (in s) with which the
-adjustment algorithm is called, to a non-zero value (if set to a negative
-value by the user, the model will set it to the tracer time step). The other
-option is to parameterize convection with implicit vertical diffusion. To do
-this, set the logical variable \textbf{implicitDiffusion }to '.\texttt{TRUE}%
-.' and the real variable \textbf{ivdc\_kappa }to a value (in m$^{2}$/s) you
-wish the tracer vertical diffusivities to have when mixing tracers
-vertically due to static instabilities. Note that \textbf{cadjFreq }and 
-\textbf{ivdc\_kappa }can not both have non-zero value.
+\end{description}
 
 \subsection{Simulation controls}
 
@@ -1180,33 +1294,35 @@
 Frequency of checkpointing and dumping of the model state are referenced to
 this clock (see below).
 
-\begin{itemize}
-\item run duration
-\end{itemize}
-
-The beginning of a simulation is set by specifying a start time (in s)
-through the real variable \textbf{startTime }or by specifying an initial
-iteration number through the integer variable \textbf{nIter0}. If these
-variables are set to nonzero values, the model will look for a ''pickup''
-file \textit{pickup.0000nIter0 }to restart the integration\textit{. }The end
-of a simulation is set through the real variable \textbf{endTime }(in s).
-Alternatively, you can specify instead the number of time steps to execute
-through the integer variable \textbf{nTimeSteps}. 
+\begin{description}
+\item[run duration] \ 
+  
+  The beginning of a simulation is set by specifying a start time (in
+  s) through the real variable \textbf{startTime }or by specifying an
+  initial iteration number through the integer variable
+  \textbf{nIter0}. If these variables are set to nonzero values, the
+  model will look for a ''pickup'' file \textit{pickup.0000nIter0 }to
+  restart the integration\textit{. }The end of a simulation is set
+  through the real variable \textbf{endTime }(in s).  Alternatively,
+  you can specify instead the number of time steps to execute through
+  the integer variable \textbf{nTimeSteps}.
+
+\item[frequency of output] \
+  
+  Real variables defining frequencies (in s) with which output files
+  are written on disk need to be set up. \textbf{dumpFreq }controls
+  the frequency with which the instantaneous state of the model is
+  saved. \textbf{chkPtFreq } and \textbf{pchkPtFreq }control the
+  output frequency of rolling and permanent checkpoint files,
+  respectively. See section 1.5.1 Output files for the definition of
+  model state and checkpoint files. In addition, time-averaged fields
+  can be written out by setting the variable \textbf{taveFreq} (in s).
+  The precision with which to write the binary data is controlled by
+  the integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32}
+  or \texttt{ 64}).
 
-\begin{itemize}
-\item frequency of output
-\end{itemize}
+\end{description}
 
-Real variables defining frequencies (in s) with which output files are
-written on disk need to be set up. \textbf{dumpFreq }controls the frequency
-with which the instantaneous state of the model is saved. \textbf{chkPtFreq }%
-and \textbf{pchkPtFreq }control the output frequency of rolling and
-permanent checkpoint files, respectively. See section 1.5.1 Output files for the
-definition of model state and checkpoint files. In addition, time-averaged
-fields can be written out by setting the variable \textbf{taveFreq} (in s).
-The precision with which to write the binary data is controlled by the
-integer variable w\textbf{riteBinaryPrec }(set it to \texttt{32} or \texttt{%
-64}).
 
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