/[MITgcm]/manual/s_getstarted/text/getting_started.tex

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-revision 1.15 by edhill,
Wed Jan 28 20:50:14 2004 UTC
+revision 1.16 by edhill,
Thu Jan 29 03:02:33 2004 UTC
 Line 39 
 http://mitgcm.org/pipermail/mitgcm-suppo
  \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}
-Line 108 
 To obtain the latest sources type:
+Line 109 
 To obtain the latest sources type:
  \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
-Line 116 
 that one may easily view the state of fi
+Line 117 
 that one may easily view the state of fi
  development milestones:
  \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
  \begin{verbatim}
- http://mitgcm.org/source_code.html
+ http://mitgcm.org/source\_code.html
  \end{verbatim}
  \begin{rawhtml} </A> \end{rawhtml}
-Line 161 
 your copy instead of downloading the ent
+Line 162 
 your copy instead of downloading the ent
  \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
-Line 383 
 Each example directory has the following
+Line 384 
 Each example directory has the following
  \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}
+   \begin{itemize}
- \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
+   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
-   the ``execution environment'' part of the code. The default version
+     the ``execution environment'' part of the code. The default
-   is located in \textit{eesupp/inc}.
+     version is located in \textit{eesupp/inc}.
- \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to the
+   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to
-   ``numerical model'' part of the code. The default version is located
+     the ``numerical model'' part of the code. The default version is
-   in \textit{model/inc}.
+     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}
+   \begin{itemize}
- \item \textit{input/data}: this file, written as a namelist, specifies
+   \item \textit{input/data}: this file, written as a namelist,
-   the main parameters for the experiment.
+     specifies the main parameters for the experiment.
- \item \textit{input/data.pkg}: contains parameters relative to the
+   \item \textit{input/data.pkg}: contains parameters relative to the
-   packages used in the experiment.
+     packages used in the experiment.
- \item \textit{input/eedata}: this file contains ``execution
+   \item \textit{input/eedata}: this file contains ``execution
-   environment'' data. At present, this consists of a specification of
+     environment'' data. At present, this consists of a specification
-   the number of threads to use in $X$ and $Y$ under multithreaded
+     of the number of threads to use in $X$ and $Y$ under multithreaded
-   execution.
+     execution.
- \end{itemize}
+   \end{itemize}
- In addition, you will also find in this directory the forcing and topography
+ In addition, you will also find in this directory the forcing and
- files as well as the files describing the initial state of the experiment.
+ topography files as well as the files describing the initial state of
- This varies from experiment to experiment. See section 2 for more details.
+ 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
+ \item \textit{results}: this directory contains the output file
- comparison with your own output when you run the experiment.
+   \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
-Line 437 
 the code.
+Line 441 
 the code.
  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
+ dependencies. We supply a script ({\em genmake2}), described in
- \ref{sect:genmake}, that automatically creates the {\em Makefile} for
+ section \ref{sect:genmake}, that automatically creates the {\em
- you. You then need to build the dependencies and compile the code.
+   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
+ \textit{verification/exp2}. The are multiple ways and places to
- do this but here let's build the code in
+ 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
+ On many systems, the {\em genmake2} program will be able to
- to use the following options when invoking \textit{genmake}:
+ 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
+ This modifies the {\em Makefile} by attaching a [long] list of files
- which other files depend. The purpose of this is to reduce
+ upon which other files depend. The purpose of this is to reduce
- re-compilation if and when you start to modify the code. {\tt make
+ re-compilation if and when you start to modify the code. The {\tt make
- depend} also created links from the model source to this directory.
+   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:
-Line 492 
 executable in the {\em input} directory
+Line 515 
 executable in the {\em input} directory
  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
+ The following sections outline some possible methods of organizing
- source and data.
+ 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}
-Line 531 
 within {\em verification/exp2/}:
+Line 555 
 within {\em verification/exp2/}:
  % cd verification/exp2
  % mkdir build
  % cd build
- % ../../../tools/genmake -mods=../code
+ % ../../../tools/genmake2 -mods=../code
  % make depend
  % make
  \end{verbatim}
-Line 553 
 running in a new directory each time mig
+Line 577 
 running in a new directory each time mig
  % ./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
-Line 561 
 scratch disk. Assuming the model source
+Line 585 
 scratch disk. Assuming the model source
  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}
-Line 577 
 the one experiment:
+Line 602 
 the one experiment:
  % 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 ../
-Line 588 
 the one experiment:
+Line 614 
 the one experiment:
- \subsection{\textit{genmake}}
+ \subsection{Using \textit{genmake2}}
  \label{sect:genmake}
- To compile the code, use the script \textit{genmake} located in the \textit{%
+ To compile the code, first use the program \texttt{genmake2} (located
- tools} directory. \textit{genmake} is a script that generates the makefile.
+ in the \textit{tools} directory) to generate a Makefile.
- It has been written so that the code can be compiled on a wide diversity of
+ \texttt{genmake2} is a shell script written to work with all
- machines and systems. However, if it doesn't work the first time on your
+ ``sh''--compatible shells including bash v1, bash v2, and Bourne.
- platform, you might need to edit certain lines of \textit{genmake} in the
+ Internally, \texttt{genmake2} determines the locations of needed
- section containing the setups for the different machines. The file is
+ files, the compiler, compiler options, libraries, and Unix tools.  It
- structured like this:
+ relies upon a number of ``optfiles'' located in the {\em
- \begin{verbatim}
+   tools/build\_options} directory.
-         .
-         .
+ The purpose of the optfiles is to provide all the compilation options
-         .
+ for particular ``platforms'' (where ``platform'' roughly means the
- general instructions (machine independent)
+ 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
-     - setup machine 1
+ optfiles shipped with the code is
-     - setup machine 2
+ \begin{center}
-     - setup machine 3
+   {\bf OS\_HARDWARE\_COMPILER }
-     - setup machine 4
+ \end{center}
-        etc
+ where
-         .
+ \begin{description}
-         .
+ \item[OS] is the name of the operating system (generally the
-         .
+   lower-case output of the {\tt 'uname'} command)
- \end{verbatim}
+ \item[HARDWARE] is a string that describes the CPU type and
+   corresponds to output from the  {\tt 'uname -m'} command:
- For example, the setup corresponding to a DEC alpha machine is reproduced
+   \begin{description}
- here:
+   \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686,
- \begin{verbatim}
+     and athlon
-   case OSF1+mpi:
+   \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2)
-     echo "Configuring for DEC Alpha"
+   \item[amd64] is AMD x86\_64 systems
-     set CPP        = ( '/usr/bin/cpp -P' )
+   \item[ppc] is for Mac PowerPC systems
-     set DEFINES    = ( ${DEFINES}  '-DTARGET_DEC -DWORDLENGTH=1' )
+   \end{description}
-     set KPP        = ( 'kapf' )
+ \item[COMPILER] is the compiler name (generally, the name of the
-     set KPPFILES   = ( 'main.F' )
+   FORTRAN executable)
-     set KFLAGS1    = ( '-scan=132 -noconc -cmp=' )
+ \end{description}
-     set FC         = ( 'f77' )
-     set FFLAGS     = ( '-convert big_endian -r8 -extend_source -automatic -call_shared -notransform_loops -align dcommons' )
+ In many cases, the default optfiles are sufficient and will result in
-     set FOPTIM     = ( '-O5 -fast -tune host -inline all' )
+ usable Makefiles.  However, for some machines or code configurations,
-     set NOOPTFLAGS = ( '-O0' )
+ new ``optfiles'' must be written. To create a new optfile, it is
-     set LIBS       = ( '-lfmpi -lmpi -lkmp_osfp10 -pthread' )
+ generally best to start with one of the defaults and modify it to suit
-     set NOOPTFILES = ( 'barrier.F different_multiple.F external_fields_load.F')
+ your needs.  Like \texttt{genmake2}, the optfiles are all written
-     set RMFILES    = ( '*.p.out' )
+ using a simple ``sh''--compatible syntax.  While nearly all variables
-     breaksw
+ used within \texttt{genmake2} may be specified in the optfiles, the
- \end{verbatim}
+ critical ones that should be defined are:
- Typically, these are the lines that you might need to edit to make \textit{%
+ \begin{description}
- genmake} work on your platform if it doesn't work the first time. \textit{%
+ \item[FC] the FORTRAN compiler (executable) to use
- genmake} understands several options that are described here:
+ \item[DEFINES] the command-line DEFINE options passed to the compiler
+ \item[CPP] the C pre-processor to use
- \begin{itemize}
+ \item[NOOPTFLAGS] options flags for special files that should not be
- \item -rootdir=dir
+   optimized
+ \end{description}
- 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{%
+ For example, the optfile for a typical Red Hat Linux machine (``ia32''
- bin} directory (which is the default compilation directory) or within the
+ architecture) using the GCC (g77) compiler is
- \textit{verification} tree.
+ \begin{verbatim}
+ FC=g77
- \item -mods=dir1,dir2,...
+ DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
+ CPP='cpp  -traditional -P'
- indicates the relative or absolute paths directories where the sources
+ NOOPTFLAGS='-O0'
- should take precedence over the default versions (located in \textit{model},
+ #  For IEEE, use the "-ffloat-store" option
- \textit{eesupp},...). Typically, this option is used when running the
+ if test "x$IEEE" = x ; then
- examples, see below.
+     FFLAGS='-Wimplicit -Wunused -Wuninitialized'
+     FOPTIM='-O3 -malign-double -funroll-loops'
- \item -enable=pkg1,pkg2,...
+ else
+     FFLAGS='-Wimplicit -Wunused -ffloat-store'
- enables packages source code \textit{pkg1}, \textit{pkg2},... when creating
+     FOPTIM='-O0 -malign-double'
- the makefile.
+ fi
+ \end{verbatim}
- \item -disable=pkg1,pkg2,...
+ If you write an optfile for an unrepresented machine or compiler, you
- disables packages source code \textit{pkg1}, \textit{pkg2},... when creating
+ are strongly encouraged to submit the optfile to the MITgcm project
- the makefile.
+ for inclusion.  Please send the file to the
+ \begin{rawhtml} <A href="mail-to:MITgcm-support@mitgcm.org"> \end{rawhtml}
- \item -platform=machine
+ \begin{center}
+   MITgcm-support@mitgcm.org
- specifies the platform for which you want the makefile. In general, you
+ \end{center}
- won't need this option. \textit{genmake} will select the right machine for
+ \begin{rawhtml} </A> \end{rawhtml}
- you (the one you're working on!). However, this option is useful if you have
+ mailing list.
- 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
+ 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
+ \end{description}
- 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}.
  \section{Running the model}

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