--- 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 03:02:33 1.16
@@ -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 1.16 2004/01/29 03:02:33 edhill Exp $
% $Name: $
%\section{Getting started}
@@ -39,6 +39,7 @@
\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}
@@ -108,7 +109,7 @@
\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
@@ -116,7 +117,7 @@
development milestones:
\begin{rawhtml} \end{rawhtml}
\begin{verbatim}
-http://mitgcm.org/source_code.html
+http://mitgcm.org/source\_code.html
\end{verbatim}
\begin{rawhtml} \end{rawhtml}
@@ -161,9 +162,9 @@
\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
@@ -383,49 +384,52 @@
\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.
-\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{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
@@ -437,44 +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
-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 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 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 +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}
@@ -531,7 +555,7 @@
% cd verification/exp2
% mkdir build
% cd build
-% ../../../tools/genmake -mods=../code
+% ../../../tools/genmake2 -mods=../code
% make depend
% make
\end{verbatim}
@@ -553,7 +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
@@ -561,7 +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}
@@ -577,7 +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 ../
@@ -588,107 +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).
+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.
-\item -jam
+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.
-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}