--- manual/s_getstarted/text/getting_started.tex 2001/10/15 19:36:09 1.5
+++ manual/s_getstarted/text/getting_started.tex 2004/01/29 03:02:33 1.16
@@ -1,4 +1,4 @@
-% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.5 2001/10/15 19:36:09 adcroft Exp $
+% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.16 2004/01/29 03:02:33 edhill Exp $
% $Name: $
%\section{Getting started}
@@ -18,82 +18,214 @@
\section{Where to find information}
\label{sect:whereToFindInfo}
-A web site is maintained for release 1 (Sealion) of MITgcm:
+A web site is maintained for release 2 (``Pelican'') of MITgcm:
+\begin{rawhtml} \end{rawhtml}
\begin{verbatim}
-http://mitgcm.org/sealion
+http://mitgcm.org/pelican
\end{verbatim}
+\begin{rawhtml} \end{rawhtml}
Here you will find an on-line version of this document, a
``browsable'' copy of the code and a searchable database of the model
and site, as well as links for downloading the model and
-documentation, to data-sources and other related sites.
+documentation, to data-sources, and other related sites.
-There is also a support news group for the model that you can email at
-\texttt{support@mitgcm.org} or browse at:
+There is also a web-archived support mailing list for the model that
+you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
+\begin{rawhtml} \end{rawhtml}
\begin{verbatim}
-news://mitgcm.org/mitgcm.support
+http://mitgcm.org/mailman/listinfo/mitgcm-support/
+http://mitgcm.org/pipermail/mitgcm-support/
\end{verbatim}
-A mail to the email list will reach all the developers and be archived
-on the newsgroup. A users email list will be established at some time
-in the future.
+\begin{rawhtml} \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} \end{rawhtml}
+\begin{verbatim}
+http://mitgcm.org/htdig/
+\end{verbatim}
+\begin{rawhtml} \end{rawhtml}
+%%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org
+
\section{Obtaining the code}
\label{sect:obtainingCode}
+MITgcm can be downloaded from our system by following
+the instructions below. As a courtesy we ask that you send e-mail to us at
+\begin{rawhtml} \end{rawhtml}
+MITgcm-support@mitgcm.org
+\begin{rawhtml} \end{rawhtml}
+to enable us to keep track of who's using the model and in what application.
+You can download the model two ways:
+
+\begin{enumerate}
+\item Using CVS software. CVS is a freely available source code management
+tool. To use CVS you need to have the software installed. Many systems
+come with CVS pre-installed, otherwise good places to look for
+the software for a particular platform are
+\begin{rawhtml} \end{rawhtml}
+cvshome.org
+\begin{rawhtml} \end{rawhtml}
+and
+\begin{rawhtml} \end{rawhtml}
+wincvs.org
+\begin{rawhtml} \end{rawhtml}
+.
+
+\item Using a tar file. This method is simple and does not
+require any special software. However, this method does not
+provide easy support for maintenance updates.
+
+\end{enumerate}
+
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
track of your changes. If CVS is not available on your machine, you can also
download a tar file.
-Before you can use CVS, the following environment variable has to be set in
-your .cshrc or .tcshrc:
+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
\begin{verbatim}
-% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
-% cvs login ( CVS password: cvsanon )
+% setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
\end{verbatim}
+in your .cshrc or .tcshrc file. For bash or sh shells, put:
+\begin{verbatim}
+% export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
+\end{verbatim}
+in your .profile or .bashrc file.
+
-You only need to do ``cvs login'' once. To obtain the source for the release:
+To get MITgcm through CVS, first register with the MITgcm CVS server
+using command:
\begin{verbatim}
-% cvs co -d directory -P -r release1 MITgcmUV
+% cvs login ( CVS password: cvsanon )
\end{verbatim}
+You only need to do a ``cvs login'' once.
-This creates a directory called \textit{directory}. If \textit{directory}
-exists this command updates your code based on the repository. Each
-directory in the source tree contains a directory \textit{CVS}. This
-information is required by CVS to keep track of your file versions with
-respect to the repository. Don't edit the files in \textit{CVS}! To obtain a
-different \textit{version} that is not the latest source:
+To obtain the latest sources type:
+\begin{verbatim}
+% cvs co MITgcm
+\end{verbatim}
+or to get a specific release type:
\begin{verbatim}
-% cvs co -d directory -P -r version MITgcm
+% cvs co -P -r checkpoint52i_post MITgcm
\end{verbatim}
-or the latest development version:
+The MITgcm web site contains further directions concerning the source
+code and CVS. It also contains a web interface to our CVS archive so
+that one may easily view the state of files, revisions, and other
+development milestones:
+\begin{rawhtml} \end{rawhtml}
\begin{verbatim}
-% cvs co -d directory -P MITgcm
+http://mitgcm.org/source\_code.html
\end{verbatim}
+\begin{rawhtml} \end{rawhtml}
+
+
+The checkout process creates a directory called \textit{MITgcm}. If
+the directory \textit{MITgcm} exists this command updates your code
+based on the repository. Each directory in the source tree contains a
+directory \textit{CVS}. This information is required by CVS to keep
+track of your file versions with respect to the repository. Don't edit
+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} \end{rawhtml}
+here
+\begin{rawhtml} \end{rawhtml}
+.
+
\paragraph*{Conventional download method}
\label{sect:conventionalDownload}
If you do not have CVS on your system, you can download the model as a
-tar file from the reference web site at:
+tar file from the web site at:
+\begin{rawhtml} \end{rawhtml}
\begin{verbatim}
http://mitgcm.org/download/
\end{verbatim}
+\begin{rawhtml} \end{rawhtml}
The tar file still contains CVS information which we urge you not to
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.
+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.
+
+\paragraph*{Upgrading from an earlier version}
+
+If you already have an earlier version of the code you can ``upgrade''
+your copy instead of downloading the entire repository again. First,
+``cd'' (change directory) to the top of your working copy:
+\begin{verbatim}
+% cd MITgcm
+\end{verbatim}
+and then issue the cvs update command such as:
+\begin{verbatim}
+% cvs -q update -r checkpoint52i_post -d -P
+\end{verbatim}
+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
+will try to merge your changes with the upgrades. If there is a
+conflict between your modifications and the upgrade, it will report
+that file with a ``C'' in front, e.g.:
+\begin{verbatim}
+C model/src/ini_parms.F
+\end{verbatim}
+If the list of conflicts scrolled off the screen, you can re-issue the
+cvs update command and it will report the conflicts. Conflicts are
+indicated in the code by the delimites ``$<<<<<<<$'', ``======='' and
+``$>>>>>>>$''. For example,
+\begin{verbatim}
+<<<<<<< ini_parms.F
+ & bottomDragLinear,myOwnBottomDragCoefficient,
+=======
+ & 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:
+\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.
+
+\paragraph*{Upgrading to the current pre-release version}
+
+We don't make a ``release'' for every little patch and bug fix in
+order to keep the frequency of upgrades to a minimum. However, if you
+have run into a problem for which ``we have already fixed in the
+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
+\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
+very latest version. As a rule, we don't recommend this since you
+might upgrade while we are in the processes of checking in the code so
+that you may only have part of a patch. Using this method of updating
+also means we can't tell what version of the code you are working
+with. So please be sure you understand what you're doing.
\section{Model and directory structure}
-The ``numerical'' model is contained within a execution environment support
-wrapper. This wrapper is designed to provide a general framework for
-grid-point models. MITgcmUV is a specific numerical model that uses the
-framework. Under this structure the model is split into execution
-environment support code and conventional numerical model code. The
-execution environment support code is held under the \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
+The ``numerical'' model is contained within a execution environment
+support wrapper. This wrapper is designed to provide a general
+framework for grid-point models. MITgcmUV is a specific numerical
+model that uses the framework. Under this structure the model is split
+into execution environment support code and conventional numerical
+model code. The execution environment support code is held under the
+\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%
@@ -106,7 +238,7 @@
\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
+\textit{src} that contain include files (*.\textit{h} files) and Fortran
subroutines (*.\textit{F} files), respectively.
\item \textit{doc}: contains brief documentation notes.
@@ -127,7 +259,7 @@
in detail in section 3.
\item \textit{tools}: this directory contains various useful tools. For
-example, \textit{genmake} is a script written in csh (C-shell) that should
+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.
@@ -147,66 +279,104 @@
\section{Example experiments}
\label{sect:modelExamples}
-Now that you have successfully downloaded the model code we recommend that
-you first try to run the examples provided with the base version. You will
-probably want to run the example that is the closest to the configuration
-you will use eventually. The examples are located in subdirectories under
-the directory \textit{verification} and are briefly described below (a full
-description is given in section 2):
+%% a set of twenty-four pre-configured numerical experiments
-\subsection{List of model examples}
+The MITgcm distribution comes with more than a dozen pre-configured
+numerical experiments. Some of these example experiments are tests of
+individual parts of the model code, but many are fully fledged
+numerical simulations. A few of the examples are used for tutorial
+documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.
+The other examples follow the same general structure as the tutorial
+examples. However, they only include brief instructions in a text file
+called {\it README}. The examples are located in subdirectories under
+the directory \textit{verification}. Each example is briefly described
+below.
-\begin{itemize}
-\item \textit{exp0} - single layer, ocean double gyre (barotropic with
-free-surface).
+\subsection{Full list of model examples}
-\item \textit{exp1} - 4 layers, ocean double gyre.
+\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}.
+\item \textit{exp1} - Four layer, ocean double gyre. This experiment
+ is described in detail in section \ref{sect:eg-baroc}.
+
\item \textit{exp2} - 4x4 degree global ocean simulation with steady
-climatological forcing.
+ climatological forcing. This experiment is described in detail in
+ section \ref{sect:eg-global}.
+
+\item \textit{exp4} - Flow over a Gaussian bump in open-water or
+ channel with open boundaries.
+
+\item \textit{exp5} - Inhomogenously forced ocean convection in a
+ doubly periodic box.
-\item \textit{exp4} - flow over a Gaussian bump in open-water or channel
-with open boundaries.
-
-\item \textit{exp5} - inhomogenously forced ocean convection in a doubly
-periodic box.
-
-\item \textit{front\_relax} - relaxation of an ocean thermal front (test for
+\item \textit{front\_relax} - Relaxation of an ocean thermal front (test for
Gent/McWilliams scheme). 2D (Y-Z).
-\item \textit{internal wave} - ocean internal wave forced by open boundary
-conditions.
-
-\item \textit{natl\_box} - eastern subtropical North Atlantic with KPP
-scheme; 1 month integration
-
-\item \textit{hs94.1x64x5} - zonal averaged atmosphere using Held and Suarez
-'94 forcing.
-
-\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and Suarez
-'94 forcing.
-
+\item \textit{internal wave} - Ocean internal wave forced by open
+ boundary conditions.
+
+\item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP
+ scheme; 1 month integration
+
+\item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and
+ Suarez '94 forcing.
+
+\item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and
+ Suarez '94 forcing.
+
\item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
-Suarez '94 forcing on the cubed sphere.
-
-\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics, 5 layers
-Molteni physics package. Global Zonal Mean configuration, 1x64x5 resolution.
-
-\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate Atmospheric
-physics, 5 layers Molteni physics package. Equatorial Slice configuration.
-2D (X-Z).
-
+ Suarez '94 forcing on the cubed sphere.
+
+\item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.
+ Global Zonal Mean configuration, 1x64x5 resolution.
+
+\item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate
+ Atmospheric physics, equatorial Slice configuration. 2D (X-Z).
+
\item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric
-physics, 5 layers Molteni physics package. 3D Equatorial Channel
-configuration (not completely tested).
+ physics. 3D Equatorial Channel configuration.
+
+\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.
+ Global configuration, on latitude longitude grid with 128x64x5 grid
+ points ($2.8^\circ{\rm degree}$ resolution).
+
+\item \textit{adjustment.128x64x1} Barotropic adjustment problem on
+ latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm
+ degree}$ resolution).
+
+\item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on
+ cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm
+ degree}$ resolution).
+
+\item \textit{advect\_cs} Two-dimensional passive advection test on
+ cube sphere grid.
+
+\item \textit{advect\_xy} Two-dimensional (horizontal plane) passive
+ advection test on Cartesian grid.
+
+\item \textit{advect\_yz} Two-dimensional (vertical plane) passive
+ advection test on Cartesian grid.
+
+\item \textit{carbon} Simple passive tracer experiment. Includes
+ derivative calculation. Described in detail in section
+ \ref{sect:eg-carbon-ad}.
+
+\item \textit{flt\_example} Example of using float package.
+
+\item \textit{global\_ocean.90x40x15} Global circulation with GM, flux
+ boundary conditions and poles.
+
+\item \textit{global\_ocean\_pressure} Global circulation in pressure
+ coordinate (non-Boussinesq ocean model). Described in detail in
+ section \ref{sect:eg-globalpressure}.
+
+\item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube
+ sphere grid.
-\item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics, 5 layers
-Molteni physics package. Global configuration, 128x64x5 resolution.
-
-\item \textit{adjustment.128x64x1}
-
-\item \textit{adjustment.cs-32x32x1}
-\end{itemize}
+\end{enumerate}
\subsection{Directory structure of model examples}
@@ -214,47 +384,52 @@
\begin{itemize}
\item \textit{code}: contains the code particular to the example. At a
-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}.
-
-\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.
+ minimum, this directory includes the following files:
-\item \textit{input}: contains the input data files required to run the
-example. At a mimimum, 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.
-\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.
+ \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{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.
+ \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
@@ -266,44 +441,63 @@
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
-dependancies. 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 dependancies 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 MITgcm-support 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 dependancies:
+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:
@@ -321,17 +515,18 @@
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}
@@ -342,7 +537,7 @@
% cp ../code/mitgcmuv ./
% ./mitgcmuv > output.txt
\end{verbatim}
-or if you will be making muliple runs with the same executable:
+or if you will be making multiple runs with the same executable:
\begin{verbatim}
% cd ../
% cp -r input run1
@@ -354,13 +549,13 @@
\subsubsection{Building from a new directory}
Since the {\em input} directory contains input files it is often more
-useful to keep {\em input} prestine and build in a new directory
+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/genmake -mods=../code
+% ../../../tools/genmake2 -mods=../code
% make depend
% make
\end{verbatim}
@@ -382,7 +577,7 @@
% ./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
@@ -390,7 +585,8 @@
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}
@@ -406,7 +602,8 @@
% 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 ../
@@ -417,107 +614,166 @@
-\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.
-
-\item -platform=machine
-
-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).
-
-\item -mpi
-
-this is used when you want to run the model in parallel processing mode
-under mpi (see section on parallel computation for more details).
-
-\item -jam
-
-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}
-
-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}.
+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}
+
+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} \end{rawhtml}
+\begin{center}
+ MITgcm-support@mitgcm.org
+\end{center}
+\begin{rawhtml} \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[--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[--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[--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[--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[--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[--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.
+
+\end{description}
+
\section{Running the model}
@@ -740,43 +996,70 @@
\item time-discretization
\end{itemize}
-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}.'.
+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}
-First, because the model equations are written in terms of perturbations, a
-reference thermodynamic state needs to be specified. This is done through
-the 1D arrays \textbf{tRef}\textit{\ }and \textbf{sRef}. \textbf{tRef }%
-specifies the reference potential temperature profile (in $^{o}$C for
-the ocean and $^{o}$K for the atmosphere) starting from the level
-k=1. Similarly, \textbf{sRef}\textit{\ }specifies the reference salinity
-profile (in ppt) for the ocean or the reference specific humidity profile
-(in g/kg) for the atmosphere.
-
-The form of the equation of state is controlled by the character variables
-\textbf{buoyancyRelation}\textit{\ }and \textbf{eosType}\textit{. }\textbf{%
-buoyancyRelation}\textit{\ }is set to '\texttt{OCEANIC}' by default and
-needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations. In
-this case, \textbf{eosType}\textit{\ }must be set to '\texttt{IDEALGAS}'.
-For the ocean, two forms of the equation of state are available: linear (set
-\textbf{eosType}\textit{\ }to '\texttt{LINEAR}') and a polynomial
-approximation to the full nonlinear equation ( set \textbf{eosType}\textit{\
-}to '\texttt{POLYNOMIAL}'). In the linear case, you need to specify the
-thermal and haline expansion coefficients represented by the variables
-\textbf{tAlpha}\textit{\ }(in K$^{-1}$) and \textbf{sBeta}\textit{\ }(in ppt$%
-^{-1}$). For the nonlinear case, you need to generate a file of polynomial
-coefficients called \textit{POLY3.COEFFS. }To do this, use the program
-\textit{utils/knudsen2/knudsen2.f }under the model tree (a Makefile is
-available in the same directory and you will need to edit the number and the
-values of the vertical levels in \textit{knudsen2.f }so that they match
-those of your configuration). \textit{\ }
+First, because the model equations are written in terms of
+perturbations, a reference thermodynamic state needs to be specified.
+This is done through the 1D arrays \textbf{tRef} and \textbf{sRef}.
+\textbf{tRef} specifies the reference potential temperature profile
+(in $^{o}$C for the ocean and $^{o}$K for the atmosphere) starting
+from the level k=1. Similarly, \textbf{sRef} specifies the reference
+salinity profile (in ppt) for the ocean or the reference specific
+humidity profile (in g/kg) for the atmosphere.
+
+The form of the equation of state is controlled by the character
+variables \textbf{buoyancyRelation} and \textbf{eosType}.
+\textbf{buoyancyRelation} is set to '\texttt{OCEANIC}' by default and
+needs to be set to '\texttt{ATMOSPHERIC}' for atmosphere simulations.
+In this case, \textbf{eosType} must be set to '\texttt{IDEALGAS}'.
+For the ocean, two forms of the equation of state are available:
+linear (set \textbf{eosType} to '\texttt{LINEAR}') and a polynomial
+approximation to the full nonlinear equation ( set
+\textbf{eosType}\textit{\ }to '\texttt{POLYNOMIAL}'). In the linear
+case, you need to specify the thermal and haline expansion
+coefficients represented by the variables \textbf{tAlpha}\textit{\
+ }(in K$^{-1}$) and \textbf{sBeta} (in ppt$^{-1}$). For the nonlinear
+case, you need to generate a file of polynomial coefficients called
+\textit{POLY3.COEFFS}. To do this, use the program
+\textit{utils/knudsen2/knudsen2.f} under the model tree (a Makefile is
+available in the same directory and you will need to edit the number
+and the values of the vertical levels in \textit{knudsen2.f} so that
+they match those of your configuration).
+
+There there are also higher polynomials for the equation of state:
+\begin{description}
+\item['\texttt{UNESCO}':] The UNESCO equation of state formula of
+ Fofonoff and Millard \cite{fofonoff83}. This equation of state
+ assumes in-situ temperature, which is not a model variable; \emph{its use
+ is therefore discouraged, and it is only listed for completeness}.
+\item['\texttt{JMD95Z}':] A modified UNESCO formula by Jackett and
+ McDougall \cite{jackett95}, which uses the model variable potential
+ temperature as input. The '\texttt{Z}' indicates that this equation
+ of state uses a horizontally and temporally constant pressure
+ $p_{0}=-g\rho_{0}z$.
+\item['\texttt{JMD95P}':] A modified UNESCO formula by Jackett and
+ McDougall \cite{jackett95}, which uses the model variable potential
+ temperature as input. The '\texttt{P}' indicates that this equation
+ of state uses the actual hydrostatic pressure of the last time
+ step. Lagging the pressure in this way requires an additional pickup
+ file for restarts.
+\item['\texttt{MDJWF}':] The new, more accurate and less expensive
+ equation of state by McDougall et~al. \cite{mcdougall03}. It also
+ requires lagging the pressure and therefore an additional pickup
+ file for restarts.
+\end{description}
+For none of these options an reference profile of temperature or
+salinity is required.
\subsection{Momentum equations}
@@ -1009,3 +1292,8 @@
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}).
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End: