--- manual/s_getstarted/text/customization.tex	2004/10/14 14:54:24	1.2
+++ manual/s_getstarted/text/customization.tex	2010/08/30 23:09:20	1.11
@@ -1,4 +1,8 @@
-\section[Customizing MITgcm]{Doing it yourself: customizing the code}
+\section[Customizing MITgcm]{Doing it yourself: customizing the model configuration}
+\label{sec:customize}
+\begin{rawhtml}
+<!-- CMIREDIR:customizing_mitgcm: -->
+\end{rawhtml}
 
 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
@@ -9,396 +13,6 @@
 part is covered in the parallel implementation section) and on the
 variables and parameters that you are likely to change.
 
-
-\subsection{Building/compiling the code elsewhere}
-
-In the example above (section \ref{sect: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
-entire source tree. The only requirement to do so is you have {\tt
-  genmake2} in your path or you know the absolute path to {\tt
-  genmake2}.
-
-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/genmake2
-% make depend
-% make
-\end{verbatim}
-However, to run the model the executable ({\em mitgcmuv}) and input
-files must be in the same place. If you only have one calculation to make:
-\begin{verbatim}
-% cd ../input
-% cp ../code/mitgcmuv ./
-% ./mitgcmuv > output.txt
-\end{verbatim}
-or if you will be making multiple runs with the same executable:
-\begin{verbatim}
-% cd ../
-% cp -r input run1
-% cp code/mitgcmuv run1
-% cd run1
-% ./mitgcmuv > output.txt
-\end{verbatim}
-
-\subsubsection{Building from a new directory}
-
-Since the {\em input} directory contains input files it is often more
-useful to keep {\em input} pristine and build in a new directory
-within {\em verification/exp2/}:
-\begin{verbatim}
-% cd verification/exp2
-% mkdir build
-% cd build
-% ../../../tools/genmake2 -mods=../code
-% make depend
-% make
-\end{verbatim}
-This builds the code exactly as before but this time you need to copy
-either the executable or the input files or both in order to run the
-model. For example,
-\begin{verbatim}
-% cp ../input/* ./
-% ./mitgcmuv > output.txt
-\end{verbatim}
-or if you tend to make multiple runs with the same executable then
-running in a new directory each time might be more appropriate:
-\begin{verbatim}
-% cd ../
-% mkdir run1
-% cp build/mitgcmuv run1/
-% cp input/* run1/
-% cd run1
-% ./mitgcmuv > output.txt
-\end{verbatim}
-
-\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
-scratch disk. Assuming the model source is in {\em ~/MITgcm} then the
-following commands will build the model in {\em /scratch/exp2-run1}:
-\begin{verbatim}
-% cd /scratch/exp2-run1
-% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
-  -mods=~/MITgcm/verification/exp2/code
-% make depend
-% make
-\end{verbatim}
-To run the model here, you'll need the input files:
-\begin{verbatim}
-% cp ~/MITgcm/verification/exp2/input/* ./
-% ./mitgcmuv > output.txt
-\end{verbatim}
-
-As before, you could build in one directory and make multiple runs of
-the one experiment:
-\begin{verbatim}
-% cd /scratch/exp2
-% mkdir build
-% cd build
-% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \
-  -mods=~/MITgcm/verification/exp2/code
-% make depend
-% make
-% cd ../
-% cp -r ~/MITgcm/verification/exp2/input run2
-% cd run2
-% ./mitgcmuv > output.txt
-\end{verbatim}
-
-
-\subsection{Using \texttt{genmake2}}
-\label{sect: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.
-
-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}
-
-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:
-
-\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}
-
-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.
-
-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}
-
-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{--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{--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{--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}).
-  
-\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,
-  a Bourne, POSIX, or compatible) shell.  The syntax in these
-  circumstances is:
-  \begin{center}
-    \texttt{\%  /bin/sh genmake2 -bash=/bin/sh [...options...]}
-  \end{center}
-  where \texttt{/bin/sh} can be replaced with the full path and name
-  of the desired shell.
-
-\end{description}
-
-
-\subsection{Building with MPI}
-\label{sect:mpi-build}
-
-Building MITgcm to use MPI libraries can be complicated due to the
-variety of different MPI implementations available, their dependencies
-or interactions with different compilers, and their often ad-hoc
-locations within file systems.  For these reasons, its generally a
-good idea to start by finding and reading the documentation for your
-machine(s) and, if necessary, seeking help from your local systems
-administrator.
-
-The steps for building MITgcm with MPI support are:
-\begin{enumerate}
-  
-\item Determine the locations of your MPI-enabled compiler and/or MPI
-  libraries and put them into an options file as described in Section
-  \ref{sect:genmake}.  One can start with one of the examples in:
-  \begin{rawhtml} <A
-    href="http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm/tools/build_options/">
-  \end{rawhtml}
-  \begin{center}
-    \texttt{MITgcm/tools/build\_options/}
-  \end{center}
-  \begin{rawhtml} </A> \end{rawhtml}
-  such as \texttt{linux\_ia32\_g77+mpi\_cg01} or
-  \texttt{linux\_ia64\_efc+mpi} and then edit it to suit the machine at
-  hand.  You may need help from your user guide or local systems
-  administrator to determine the exact location of the MPI libraries.
-  If libraries are not installed, MPI implementations and related
-  tools are available including:
-  \begin{itemize}
-  \item \begin{rawhtml} <A
-      href="http://www-unix.mcs.anl.gov/mpi/mpich/">
-    \end{rawhtml}
-    MPICH
-    \begin{rawhtml} </A> \end{rawhtml}
-
-  \item \begin{rawhtml} <A
-      href="http://www.lam-mpi.org/">
-    \end{rawhtml}
-    LAM/MPI
-    \begin{rawhtml} </A> \end{rawhtml}
-
-  \item \begin{rawhtml} <A
-      href="http://www.osc.edu/~pw/mpiexec/">
-    \end{rawhtml}
-    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:
-{\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:
-\begin{verbatim}
-  %  mpirun -np 4 -machinefile mf ./mitgcmuv
-\end{verbatim}
-  Sightly more complicated scripts may be needed for many machines
-  since execution of the code may be controlled by both the MPI
-  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
-  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/">
-  \end{rawhtml}
-  {\footnotesize \tt
-    http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ }
-  \begin{rawhtml} </A> \end{rawhtml}
-
-\end{enumerate}
-
-An example of the above process on the MITgcm cluster (``cg01'') using
-the GNU g77 compiler and the mpich MPI library is:
-
-{\footnotesize \begin{verbatim}
-  %  cd MITgcm/verification/exp5
-  %  mkdir build
-  %  cd build
-  %  ../../../tools/genmake2 -mpi -mods=../code \
-       -of=../../../tools/build_options/linux_ia32_g77+mpi_cg01
-  %  make depend
-  %  make
-  %  cd ../input
-  %  /usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/g77/bin/mpirun.ch_gm \
-       -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
-\end{verbatim} }
-
-\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
@@ -410,13 +24,18 @@
 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.
+part of the namelist the parameters are located. Here is a complete list 
+of the model parameters related to the main model (namelist parameters
+for the packages are located in the package descriptions), their meaning, 
+and their default values:
+
+\input{s_getstarted/text/main-parms.tex}
 
 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}
+\subsection{Parameters: Computational domain, geometry and time-discretization}
 
 \begin{description}
 \item[dimensions] \ 
@@ -435,7 +54,7 @@
   through the logical variables \textbf{usingCartesianGrid},
   \textbf{usingSphericalPolarGrid}, and \textbf{usingCurvilinearGrid}.
   In the case of spherical and curvilinear grids, the southern
-  boundary is defined through the variable \textbf{phiMin} which
+  boundary is defined through the variable \textbf{ygOrigin} 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} and \textbf{dely} (in meters in the
@@ -509,7 +128,7 @@
 \end{description}
 
 
-\subsection{Equation of state}
+\subsection{Parameters: Equation of state}
 
 First, because the model equations are written in terms of
 perturbations, a reference thermodynamic state needs to be specified.
@@ -564,7 +183,7 @@
 For none of these options an reference profile of temperature or
 salinity is required.
 
-\subsection{Momentum equations}
+\subsection{Parameters: Momentum equations}
 
 In this section, we only focus for now on the parameters that you are
 likely to change, i.e. the ones relative to forcing and dissipation
@@ -583,9 +202,19 @@
 \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).
+  The initial horizontal velocity components can be specified from 
+  binary files \textbf{uVelInitFile} and \textbf{vVelInitFile}.
+  These files should contain 3D data ordered in an (x,y,r) fashion with 
+  k=1 as the first vertical level (surface level). 
+  If no file names are provided, the velocity is initialised to zero.
+  The initial vertical velocity is always derived from the horizontal velocity
+  using the continuity equation, even in the case of non-hydrostatic simulation 
+  (see, e.g.: {\it tutorial\_deep\_convection/input/data}).
+
+  In the case of a restart (from the end of a previous simulation), 
+  the velocity field is read from a pickup file
+  (see section on simulation control parameters) 
+  and the initial velocity files are ignored.
 
 \item[forcing] \ 
   
@@ -634,9 +263,8 @@
   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} in s$ ^{-1}$) and
-  quadratic (set the variable \textbf{bottomDragQuadratic} in
-  m$^{-1}$).
+  (set the variable \textbf{bottomDragLinear} in m/s) and
+  quadratic (set the variable \textbf{bottomDragQuadratic}, dimensionless).
 
   The Fourier and Shapiro filters are described elsewhere.
 
@@ -670,7 +298,7 @@
 
 \end{description} 
 
-\subsection{Tracer equations}
+\subsection{Parameters: Tracer equations}
 
 This section covers the tracer equations i.e. the potential
 temperature equation and the salinity (for the ocean) or specific
@@ -762,7 +390,7 @@
 
 \end{description}
 
-\subsection{Simulation controls}
+\subsection{Parameters: Simulation controls}
 
 The model ''clock'' is defined by the variable \textbf{deltaTClock}
 (in s) which determines the IO frequencies and is used in tagging
