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

Diff of /manual/s_getstarted/text/getting_started.tex

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.25 by edhill, Fri Jun 4 15:32:38 2004 UTC revision 1.30 by edhill, Sat Oct 16 03:40:13 2004 UTC
# Line 15  structure are described more fully in ch Line 15  structure are described more fully in ch
15  this section, we provide information on how to customize the code when  this section, we provide information on how to customize the code when
16  you are ready to try implementing the configuration you have in mind.  you are ready to try implementing the configuration you have in mind.
17    
18    
19  \section{Where to find information}  \section{Where to find information}
20  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
21    \begin{rawhtml}
22    <!-- CMIREDIR:whereToFindInfo: -->
23    \end{rawhtml}
24    
25  A web site is maintained for release 2 (``Pelican'') of MITgcm:  A web site is maintained for release 2 (``Pelican'') of MITgcm:
26  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}
# Line 50  http://mitgcm.org/htdig/ Line 54  http://mitgcm.org/htdig/
54    
55  \section{Obtaining the code}  \section{Obtaining the code}
56  \label{sect:obtainingCode}  \label{sect:obtainingCode}
57    \begin{rawhtml}
58    <!-- CMIREDIR:obtainingCode: -->
59    \end{rawhtml}
60    
61  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
62  the instructions below. As a courtesy we ask that you send e-mail to us at  the instructions below. As a courtesy we ask that you send e-mail to us at
# Line 79  provide easy support for maintenance upd Line 86  provide easy support for maintenance upd
86    
87  \end{enumerate}  \end{enumerate}
88    
89  \subsubsection{Checkout from CVS}  \subsection{Method 1 - Checkout from CVS}
90  \label{sect:cvs_checkout}  \label{sect:cvs_checkout}
91    
92  If CVS is available on your system, we strongly encourage you to use it. CVS  If CVS is available on your system, we strongly encourage you to use it. CVS
# Line 169  they create can be changed to a differen Line 176  they create can be changed to a differen
176  \end{verbatim}  \end{verbatim}
177    
178    
179  \subsubsection{Conventional download method}  \subsection{Method 2 - Tar file download}
180  \label{sect:conventionalDownload}  \label{sect:conventionalDownload}
181    
182  If you do not have CVS on your system, you can download the model as a  If you do not have CVS on your system, you can download the model as a
# Line 256  also means we can't tell what version of Line 263  also means we can't tell what version of
263  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
264    
265  \section{Model and directory structure}  \section{Model and directory structure}
266    \begin{rawhtml}
267    <!-- CMIREDIR:directory_structure: -->
268    \end{rawhtml}
269    
270  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
271  support wrapper. This wrapper is designed to provide a general  support wrapper. This wrapper is designed to provide a general
# Line 324  structure). Line 334  structure).
334    
335  \end{itemize}  \end{itemize}
336    
337  \section{Example experiments}  \section[MITgcm Example Experiments]{Example experiments}
338  \label{sect:modelExamples}  \label{sect:modelExamples}
339    \begin{rawhtml}
340    <!-- CMIREDIR:modelExamples: -->
341    \end{rawhtml}
342    
343  %% a set of twenty-four pre-configured numerical experiments  %% a set of twenty-four pre-configured numerical experiments
344    
# Line 484  Each example directory has the following Line 497  Each example directory has the following
497  Once you have chosen the example you want to run, you are ready to  Once you have chosen the example you want to run, you are ready to
498  compile the code.  compile the code.
499    
500  \section{Building the code}  \section[Building MITgcm]{Building the code}
501  \label{sect:buildingCode}  \label{sect:buildingCode}
502    \begin{rawhtml}
503    <!-- CMIREDIR:buildingCode: -->
504    \end{rawhtml}
505    
506  To compile the code, we use the {\em make} program. This uses a file  To compile the code, we use the {\em make} program. This uses a file
507  ({\em Makefile}) that allows us to pre-process source files, specify  ({\em Makefile}) that allows us to pre-process source files, specify
# Line 507  First, build the {\em Makefile}: Line 523  First, build the {\em Makefile}:
523  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
524  \end{verbatim}  \end{verbatim}
525  The command line option tells {\em genmake} to override model source  The command line option tells {\em genmake} to override model source
526  code with any files in the directory {\em ./code/}.  code with any files in the directory {\em ../code/}.
527    
528  On many systems, the {\em genmake2} program will be able to  On many systems, the {\em genmake2} program will be able to
529  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
530  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``echo \$PATH''), and then choose an
531  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
532    tools/build\_options} directory.  Under some circumstances, a user  the {\em tools/build\_options} directory.  Under some circumstances, a
533  may have to create a new ``optfile'' in order to specify the exact  user may have to create a new ``optfile'' in order to specify the
534  combination of compiler, compiler flags, libraries, and other options  exact combination of compiler, compiler flags, libraries, and other
535  necessary to build a particular configuration of MITgcm.  In such  options necessary to build a particular configuration of MITgcm.  In
536  cases, it is generally helpful to read the existing ``optfiles'' and  such cases, it is generally helpful to read the existing ``optfiles''
537  mimic their syntax.  and mimic their syntax.
538    
539  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
540  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
# Line 542  This modifies the {\em Makefile} by atta Line 558  This modifies the {\em Makefile} by atta
558  upon which other files depend. The purpose of this is to reduce  upon which other files depend. The purpose of this is to reduce
559  re-compilation if and when you start to modify the code. The {\tt make  re-compilation if and when you start to modify the code. The {\tt make
560    depend} command also creates links from the model source to this    depend} command also creates links from the model source to this
561  directory.  directory.  It is important to note that the {\tt make depend} stage
562    will occasionally produce warnings or errors since the dependency
563    parsing tool is unable to find all of the necessary header files
564    (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it is
565    usually OK to ignore the warnings/errors and proceed to the next step.
566    
567  Next compile the code:  Next compile the code:
568  \begin{verbatim}  \begin{verbatim}
# Line 561  where we are re-directing the stream of Line 581  where we are re-directing the stream of
581  output.txt}.  output.txt}.
582    
583    
584  \subsection{Building/compiling the code elsewhere}  \section[Running MITgcm]{Running the model in prognostic mode}
   
 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} }  
   
   
   
 \section{Running the model}  
585  \label{sect:runModel}  \label{sect:runModel}
586    \begin{rawhtml}
587    <!-- CMIREDIR:runModel: -->
588    \end{rawhtml}
589    
590  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfuully (section \ref{sect:buildingCode})
591  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
592  local directory.  local directory.
593    
594  To run the model as a single process (ie. not in parallel) simply  To run the model as a single process (\textit{ie.} not in parallel)
595  type:  simply type:
596  \begin{verbatim}  \begin{verbatim}
597  % ./mitgcmuv  % ./mitgcmuv
598  \end{verbatim}  \end{verbatim}
# Line 972  normally re-direct the {\em stdout} stre Line 606  normally re-direct the {\em stdout} stre
606  \begin{verbatim}  \begin{verbatim}
607  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
608  \end{verbatim}  \end{verbatim}
609    In the event that the model encounters an error and stops, it is very
610    helpful to include the last few line of this \texttt{output.txt} file
611    along with the (\texttt{stderr}) error message within any bug reports.
612    
613  For the example experiments in {\em verification}, an example of the  For the example experiments in {\em verification}, an example of the
614  output is kept in {\em results/output.txt} for comparison. You can compare  output is kept in {\em results/output.txt} for comparison. You can
615  your {\em output.txt} with this one to check that the set-up works.  compare your {\em output.txt} with the corresponding one for that
616    experiment to check that the set-up works.
617    
618    
619    
620  \subsection{Output files}  \subsection{Output files}
621    
622  The model produces various output files. At a minimum, the instantaneous  The model produces various output files.  Depending upon the I/O
623  ``state'' of the model is written out, which is made of the following files:  package selected (either \texttt{mdsio} or \texttt{mnc} or both as
624    determined by both the compile-time settings and the run-time flags in
625    \texttt{data.pkg}), the following output may appear.
626    
627    
628    \subsubsection{MDSIO output files}
629    
630    The ``traditional'' output files are generated by the \texttt{mdsio}
631    package.  At a minimum, the instantaneous ``state'' of the model is
632    written out, which is made of the following files:
633    
634  \begin{itemize}  \begin{itemize}
635  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>
# Line 1030  as the pickup files but are named differ Line 677  as the pickup files but are named differ
677  used to restart the model but are overwritten every other time they are  used to restart the model but are overwritten every other time they are
678  output to save disk space during long integrations.  output to save disk space during long integrations.
679    
680    
681    
682    \subsubsection{MNC output files}
683    
684    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
685    is usually (though not necessarily) placed within a subdirectory with
686    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files
687    within this subdirectory are all in the ``self-describing'' netCDF
688    format and can thus be browsed and/or plotted using tools such as:
689    \begin{itemize}
690    \item At a minimum, the \texttt{ncdump} utility is typically included
691      with every netCDF install:
692      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
693    \begin{verbatim}
694    http://www.unidata.ucar.edu/packages/netcdf/
695    \end{verbatim}
696      \begin{rawhtml} </A> \end{rawhtml}
697    
698    \item The \texttt{ncview} utility is a very convenient and quick way
699      to plot netCDF data and it runs on most OSes:
700      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
701    \begin{verbatim}
702    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
703    \end{verbatim}
704      \begin{rawhtml} </A> \end{rawhtml}
705      
706    \item MatLAB(c) and other common post-processing environments provide
707      various netCDF interfaces including:
708      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
709    \begin{verbatim}
710    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
711    \end{verbatim}
712      \begin{rawhtml} </A> \end{rawhtml}
713    
714    \end{itemize}
715    
716    
717  \subsection{Looking at the output}  \subsection{Looking at the output}
718    
719  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
720  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
721  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \textit{.data} and \textit{.meta}. The
722  binary form (big\_endian by default). The \textit{.meta} file is a  \textit{.data} file contains the data written in binary form
723  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \textit{.meta} file is a ``header'' file
724  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
725  particularly useful when running multi-processors calculations. The base  \textit{.data} file. This way of organizing the output is particularly
726  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
727  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
728  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
729  the data. Look at the comments inside the script to see how to use it.  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m}
730    reads the data. Look at the comments inside the script to see how to
731    use it.
732    
733  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
734  \begin{verbatim}  \begin{verbatim}
# Line 1059  Some examples of reading and visualizing Line 745  Some examples of reading and visualizing
745  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
746  \end{verbatim}  \end{verbatim}
747    
748  \section{Doing it yourself: customizing the code}  Similar scripts for netCDF output (\texttt{rdmnc.m}) are available.
   
 When you are ready to run the model in the configuration you want, the  
 easiest thing is to use and adapt the setup of the case studies  
 experiment (described previously) that is the closest to your  
 configuration. Then, the amount of setup will be minimized. In this  
 section, we focus on the setup relative to the ``numerical model''  
 part of the code (the setup relative to the ``execution environment''  
 part is covered in the parallel implementation section) and on the  
 variables and parameters that you are likely to change.  
   
 \subsection{Configuration and setup}  
   
 The CPP keys relative to the ``numerical model'' part of the code are  
 all defined and set in the file \textit{CPP\_OPTIONS.h }in the  
 directory \textit{ model/inc }or in one of the \textit{code  
 }directories of the case study experiments under  
 \textit{verification.} The model parameters are defined and declared  
 in the file \textit{model/inc/PARAMS.h }and their default values are  
 set in the routine \textit{model/src/set\_defaults.F. }The default  
 values can be modified in the namelist file \textit{data }which needs  
 to be located in the directory where you will run the model. The  
 parameters are initialized in the routine  
 \textit{model/src/ini\_parms.F}.  Look at this routine to see in what  
 part of the namelist the parameters are located.  
   
 In what follows the parameters are grouped into categories related to  
 the computational domain, the equations solved in the model, and the  
 simulation controls.  
   
 \subsection{Computational domain, geometry and time-discretization}  
   
 \begin{description}  
 \item[dimensions] \  
     
   The number of points in the x, y, and r directions are represented  
   by the variables \textbf{sNx}, \textbf{sNy} and \textbf{Nr}  
   respectively which are declared and set in the file  
   \textit{model/inc/SIZE.h}.  (Again, this assumes a mono-processor  
   calculation. For multiprocessor calculations see the section on  
   parallel implementation.)  
   
 \item[grid] \  
     
   Three different grids are available: cartesian, spherical polar, and  
   curvilinear (which includes the cubed sphere). The grid is set  
   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  
   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  
   case of a cartesian grid, in degrees otherwise).  The vertical grid  
   spacing is set through the 1D array \textbf{delz} for the ocean (in  
   meters) or \textbf{delp} for the atmosphere (in Pa).  The variable  
   \textbf{Ro\_SeaLevel} represents the standard position of Sea-Level  
   in ``R'' coordinate. This is typically set to 0m for the ocean  
   (default value) and 10$^{5}$Pa for the atmosphere. For the  
   atmosphere, also set the logical variable \textbf{groundAtK1} to  
   \texttt{'.TRUE.'} which puts the first level (k=1) at the lower  
   boundary (ground).  
     
   For the cartesian grid case, the Coriolis parameter $f$ is set  
   through the variables \textbf{f0} and \textbf{beta} which correspond  
   to the reference Coriolis parameter (in s$^{-1}$) and  
   $\frac{\partial f}{ \partial y}$(in m$^{-1}$s$^{-1}$) respectively.  
   If \textbf{beta } is set to a nonzero value, \textbf{f0} is the  
   value of $f$ at the southern edge of the domain.  
   
 \item[topography - full and partial cells] \  
     
   The domain bathymetry is read from a file that contains a 2D (x,y)  
   map of depths (in m) for the ocean or pressures (in Pa) for the  
   atmosphere. The file name is represented by the variable  
   \textbf{bathyFile}. The file is assumed to contain binary numbers  
   giving the depth (pressure) of the model at each grid cell, ordered  
   with the x coordinate varying fastest. The points are ordered from  
   low coordinate to high coordinate for both axes. The model code  
   applies without modification to enclosed, periodic, and double  
   periodic domains. Periodicity is assumed by default and is  
   suppressed by setting the depths to 0m for the cells at the limits  
   of the computational domain (note: not sure this is the case for the  
   atmosphere). The precision with which to read the binary data is  
   controlled by the integer variable \textbf{readBinaryPrec} which can  
   take the value \texttt{32} (single precision) or \texttt{64} (double  
   precision). See the matlab program \textit{gendata.m} in the  
   \textit{input} directories under \textit{verification} to see how  
   the bathymetry files are generated for the case study experiments.  
     
   To use the partial cell capability, the variable \textbf{hFacMin}  
   needs to be set to a value between 0 and 1 (it is set to 1 by  
   default) corresponding to the minimum fractional size of the cell.  
   For example if the bottom cell is 500m thick and \textbf{hFacMin} is  
   set to 0.1, the actual thickness of the cell (i.e. used in the code)  
   can cover a range of discrete values 50m apart from 50m to 500m  
   depending on the value of the bottom depth (in \textbf{bathyFile})  
   at this point.  
     
   Note that the bottom depths (or pressures) need not coincide with  
   the models levels as deduced from \textbf{delz} or \textbf{delp}.  
   The model will interpolate the numbers in \textbf{bathyFile} so that  
   they match the levels obtained from \textbf{delz} or \textbf{delp}  
   and \textbf{hFacMin}.  
     
   (Note: the atmospheric case is a bit more complicated than what is  
   written here I think. To come soon...)  
   
 \item[time-discretization] \  
     
   The time steps are set through the real variables \textbf{deltaTMom}  
   and \textbf{deltaTtracer} (in s) which represent the time step for  
   the momentum and tracer equations, respectively. For synchronous  
   integrations, simply set the two variables to the same value (or you  
   can prescribe one time step only through the variable  
   \textbf{deltaT}). The Adams-Bashforth stabilizing parameter is set  
   through the variable \textbf{abEps} (dimensionless). The stagger  
   baroclinic time stepping can be activated by setting the logical  
   variable \textbf{staggerTimeStep} to \texttt{'.TRUE.'}.  
   
 \end{description}  
   
   
 \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} 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} to  
 \texttt{'POLYNOMIAL'}). In the linear case, you need to specify the  
 thermal and haline expansion coefficients represented by the variables  
 \textbf{tAlpha} (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; {\em 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}  
   
 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  
 for example.  The details relevant to the vector-invariant form of the  
 equations and the various advection schemes are not covered for the  
 moment. We assume that you use the standard form of the momentum  
 equations (i.e. the flux-form) with the default advection scheme.  
 Also, there are a few logical variables that allow you to turn on/off  
 various terms in the momentum equation. These variables are called  
 \textbf{momViscosity, momAdvection, momForcing, useCoriolis,  
   momPressureForcing, momStepping} and \textbf{metricTerms }and are  
 assumed to be set to \texttt{'.TRUE.'} here.  Look at the file  
 \textit{model/inc/PARAMS.h }for a precise definition of these  
 variables.  
   
 \begin{description}  
 \item[initialization] \  
     
   The velocity components are initialized to 0 unless the simulation  
   is starting from a pickup file (see section on simulation control  
   parameters).  
   
 \item[forcing] \  
     
   This section only applies to the ocean. You need to generate  
   wind-stress data into two files \textbf{zonalWindFile} and  
   \textbf{meridWindFile} corresponding to the zonal and meridional  
   components of the wind stress, respectively (if you want the stress  
   to be along the direction of only one of the model horizontal axes,  
   you only need to generate one file). The format of the files is  
   similar to the bathymetry file. The zonal (meridional) stress data  
   are assumed to be in Pa and located at U-points (V-points). As for  
   the bathymetry, the precision with which to read the binary data is  
   controlled by the variable \textbf{readBinaryPrec}.  See the matlab  
   program \textit{gendata.m} in the \textit{input} directories under  
   \textit{verification} to see how simple analytical wind forcing data  
   are generated for the case study experiments.  
     
   There is also the possibility of prescribing time-dependent periodic  
   forcing. To do this, concatenate the successive time records into a  
   single file (for each stress component) ordered in a (x,y,t) fashion  
   and set the following variables: \textbf{periodicExternalForcing }to  
   \texttt{'.TRUE.'}, \textbf{externForcingPeriod }to the period (in s)  
   of which the forcing varies (typically 1 month), and  
   \textbf{externForcingCycle} to the repeat time (in s) of the forcing  
   (typically 1 year -- note: \textbf{ externForcingCycle} must be a  
   multiple of \textbf{externForcingPeriod}).  With these variables set  
   up, the model will interpolate the forcing linearly at each  
   iteration.  
   
 \item[dissipation] \  
     
   The lateral eddy viscosity coefficient is specified through the  
   variable \textbf{viscAh} (in m$^{2}$s$^{-1}$). The vertical eddy  
   viscosity coefficient is specified through the variable  
   \textbf{viscAz} (in m$^{2}$s$^{-1}$) for the ocean and  
   \textbf{viscAp} (in Pa$^{2}$s$^{-1}$) for the atmosphere.  The  
   vertical diffusive fluxes can be computed implicitly by setting the  
   logical variable \textbf{implicitViscosity }to \texttt{'.TRUE.'}.  
   In addition, biharmonic mixing can be added as well through the  
   variable \textbf{viscA4} (in m$^{4}$s$^{-1}$). On a spherical polar  
   grid, you might also need to set the variable \textbf{cosPower}  
   which is set to 0 by default and which represents the power of  
   cosine of latitude to multiply viscosity. Slip or no-slip conditions  
   at lateral and bottom boundaries are specified through the logical  
   variables \textbf{no\_slip\_sides} and \textbf{no\_slip\_bottom}. If  
   set to \texttt{'.FALSE.'}, free-slip boundary conditions are  
   applied. If no-slip boundary conditions are applied at the bottom, a  
   bottom drag can be applied as well. Two forms are available: linear  
   (set the variable \textbf{bottomDragLinear} in s$ ^{-1}$) and  
   quadratic (set the variable \textbf{bottomDragQuadratic} in  
   m$^{-1}$).  
   
   The Fourier and Shapiro filters are described elsewhere.  
   
 \item[C-D scheme] \  
     
   If you run at a sufficiently coarse resolution, you will need the  
   C-D scheme for the computation of the Coriolis terms. The  
   variable\textbf{\ tauCD}, which represents the C-D scheme coupling  
   timescale (in s) needs to be set.  
     
 \item[calculation of pressure/geopotential] \  
     
   First, to run a non-hydrostatic ocean simulation, set the logical  
   variable \textbf{nonHydrostatic} to \texttt{'.TRUE.'}. The pressure  
   field is then inverted through a 3D elliptic equation. (Note: this  
   capability is not available for the atmosphere yet.) By default, a  
   hydrostatic simulation is assumed and a 2D elliptic equation is used  
   to invert the pressure field. The parameters controlling the  
   behaviour of the elliptic solvers are the variables  
   \textbf{cg2dMaxIters} and \textbf{cg2dTargetResidual } for  
   the 2D case and \textbf{cg3dMaxIters} and  
   \textbf{cg3dTargetResidual} for the 3D case. You probably won't need to  
   alter the default values (are we sure of this?).  
     
   For the calculation of the surface pressure (for the ocean) or  
   surface geopotential (for the atmosphere) you need to set the  
   logical variables \textbf{rigidLid} and \textbf{implicitFreeSurface}  
   (set one to \texttt{'.TRUE.'} and the other to \texttt{'.FALSE.'}  
   depending on how you want to deal with the ocean upper or atmosphere  
   lower boundary).  
   
 \end{description}  
   
 \subsection{Tracer equations}  
   
 This section covers the tracer equations i.e. the potential  
 temperature equation and the salinity (for the ocean) or specific  
 humidity (for the atmosphere) equation. As for the momentum equations,  
 we only describe for now the parameters that you are likely to change.  
 The logical variables \textbf{tempDiffusion} \textbf{tempAdvection}  
 \textbf{tempForcing}, and \textbf{tempStepping} allow you to turn  
 on/off terms in the temperature equation (same thing for salinity or  
 specific humidity with variables \textbf{saltDiffusion},  
 \textbf{saltAdvection} etc.). These variables are all assumed here to  
 be set to \texttt{'.TRUE.'}. Look at file \textit{model/inc/PARAMS.h}  
 for a precise definition.  
   
 \begin{description}  
 \item[initialization] \  
     
   The initial tracer data can be contained in the binary files  
   \textbf{hydrogThetaFile} and \textbf{hydrogSaltFile}. These files  
   should contain 3D data ordered in an (x,y,r) fashion with k=1 as the  
   first vertical level.  If no file names are provided, the tracers  
   are then initialized with the values of \textbf{tRef} and  
   \textbf{sRef} mentioned above (in the equation of state section). In  
   this case, the initial tracer data are uniform in x and y for each  
   depth level.  
   
 \item[forcing] \  
     
   This part is more relevant for the ocean, the procedure for the  
   atmosphere not being completely stabilized at the moment.  
     
   A combination of fluxes data and relaxation terms can be used for  
   driving the tracer equations.  For potential temperature, heat flux  
   data (in W/m$ ^{2}$) can be stored in the 2D binary file  
   \textbf{surfQfile}.  Alternatively or in addition, the forcing can  
   be specified through a relaxation term. The SST data to which the  
   model surface temperatures are restored to are supposed to be stored  
   in the 2D binary file \textbf{thetaClimFile}. The corresponding  
   relaxation time scale coefficient is set through the variable  
   \textbf{tauThetaClimRelax} (in s). The same procedure applies for  
   salinity with the variable names \textbf{EmPmRfile},  
   \textbf{saltClimFile}, and \textbf{tauSaltClimRelax} for freshwater  
   flux (in m/s) and surface salinity (in ppt) data files and  
   relaxation time scale coefficient (in s), respectively. Also for  
   salinity, if the CPP key \textbf{USE\_NATURAL\_BCS} is turned on,  
   natural boundary conditions are applied i.e. when computing the  
   surface salinity tendency, the freshwater flux is multiplied by the  
   model surface salinity instead of a constant salinity value.  
     
   As for the other input files, the precision with which to read the  
   data is controlled by the variable \textbf{readBinaryPrec}.  
   Time-dependent, periodic forcing can be applied as well following  
   the same procedure used for the wind forcing data (see above).  
   
 \item[dissipation] \  
     
   Lateral eddy diffusivities for temperature and salinity/specific  
   humidity are specified through the variables \textbf{diffKhT} and  
   \textbf{diffKhS} (in m$^{2}$/s). Vertical eddy diffusivities are  
   specified through the variables \textbf{diffKzT} and  
   \textbf{diffKzS} (in m$^{2}$/s) for the ocean and \textbf{diffKpT  
   }and \textbf{diffKpS} (in Pa$^{2}$/s) for the atmosphere. The  
   vertical diffusive fluxes can be computed implicitly by setting the  
   logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}.  
   In addition, biharmonic diffusivities can be specified as well  
   through the coefficients \textbf{diffK4T} and \textbf{diffK4S} (in  
   m$^{4}$/s). Note that the cosine power scaling (specified through  
   \textbf{cosPower}---see the momentum equations section) is applied to  
   the tracer diffusivities (Laplacian and biharmonic) as well. The  
   Gent and McWilliams parameterization for oceanic tracers is  
   described in the package section. Finally, note that tracers can be  
   also subject to Fourier and Shapiro filtering (see the corresponding  
   section on these filters).  
   
 \item[ocean convection] \  
     
   Two options are available to parameterize ocean convection: one is  
   to use the convective adjustment scheme. In this case, you need to  
   set the variable \textbf{cadjFreq}, which represents the frequency  
   (in s) with which the adjustment algorithm is called, to a non-zero  
   value (if set to a negative value by the user, the model will set it  
   to the tracer time step). The other option is to parameterize  
   convection with implicit vertical diffusion. To do this, set the  
   logical variable \textbf{implicitDiffusion} to \texttt{'.TRUE.'}  
   and the real variable \textbf{ivdc\_kappa} to a value (in m$^{2}$/s)  
   you wish the tracer vertical diffusivities to have when mixing  
   tracers vertically due to static instabilities. Note that  
   \textbf{cadjFreq} and \textbf{ivdc\_kappa}can not both have non-zero  
   value.  
   
 \end{description}  
   
 \subsection{Simulation controls}  
   
 The model ''clock'' is defined by the variable \textbf{deltaTClock}  
 (in s) which determines the IO frequencies and is used in tagging  
 output.  Typically, you will set it to the tracer time step for  
 accelerated runs (otherwise it is simply set to the default time step  
 \textbf{deltaT}).  Frequency of checkpointing and dumping of the model  
 state are referenced to this clock (see below).  
   
 \begin{description}  
 \item[run duration] \  
     
   The beginning of a simulation is set by specifying a start time (in  
   s) through the real variable \textbf{startTime} or by specifying an  
   initial iteration number through the integer variable  
   \textbf{nIter0}. If these variables are set to nonzero values, the  
   model will look for a ''pickup'' file \textit{pickup.0000nIter0} to  
   restart the integration. The end of a simulation is set through the  
   real variable \textbf{endTime} (in s).  Alternatively, you can  
   specify instead the number of time steps to execute through the  
   integer variable \textbf{nTimeSteps}.  
   
 \item[frequency of output] \  
     
   Real variables defining frequencies (in s) with which output files  
   are written on disk need to be set up. \textbf{dumpFreq} controls  
   the frequency with which the instantaneous state of the model is  
   saved. \textbf{chkPtFreq} and \textbf{pchkPtFreq} control the output  
   frequency of rolling and permanent checkpoint files, respectively.  
   See section 1.5.1 Output files for the definition of model state and  
   checkpoint files. In addition, time-averaged fields can be written  
   out by setting the variable \textbf{taveFreq} (in s).  The precision  
   with which to write the binary data is controlled by the integer  
   variable w\textbf{riteBinaryPrec} (set it to \texttt{32} or  
   \texttt{64}).  
   
 \end{description}  
   
   
 %%% Local Variables:  
 %%% mode: latex  
 %%% TeX-master: t  
 %%% End:  
Legend:
Removed from v.1.25  
changed lines
  Added in v.1.30
  ViewVC Help
Powered by ViewVC 1.1.22