--- manual/s_getstarted/text/getting_started.tex 2005/08/09 21:52:09 1.31 +++ manual/s_getstarted/text/getting_started.tex 2006/04/20 22:09:08 1.35 @@ -1,4 +1,4 @@ -% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.31 2005/08/09 21:52:09 edhill Exp $ +% $Header: /home/ubuntu/mnt/e9_copy/manual/s_getstarted/text/getting_started.tex,v 1.35 2006/04/20 22:09:08 molod Exp $ % $Name: $ %\section{Getting started} @@ -15,7 +15,6 @@ this section, we provide information on how to customize the code when you are ready to try implementing the configuration you have in mind. - \section{Where to find information} \label{sect:whereToFindInfo} \begin{rawhtml} @@ -126,7 +125,7 @@ code and CVS. It also contains a web interface to our CVS archive so that one may easily view the state of files, revisions, and other development milestones: -\begin{rawhtml} \end{rawhtml} +\begin{rawhtml} \end{rawhtml} \begin{verbatim} http://mitgcm.org/source_code.html \end{verbatim} @@ -163,7 +162,7 @@ the files in \texttt{CVS}! You can also use CVS to download code updates. More extensive information on using CVS for maintaining MITgcm code can be found -\begin{rawhtml} \end{rawhtml} +\begin{rawhtml} \end{rawhtml} here \begin{rawhtml} \end{rawhtml} . @@ -192,7 +191,7 @@ us if you should need to send us your copy of the code. If a recent tar file does not exist, then please contact the developers through the -\begin{rawhtml} \end{rawhtml} +\begin{rawhtml} \end{rawhtml} MITgcm-support@mitgcm.org \begin{rawhtml} \end{rawhtml} mailing list. @@ -343,16 +342,16 @@ %% a set of twenty-four pre-configured numerical experiments -The MITgcm distribution comes with more than a dozen pre-configured -numerical experiments. Some of these example experiments are tests of -individual parts of the model code, but many are fully fledged -numerical simulations. A few of the examples are used for tutorial -documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}. -The other examples follow the same general structure as the tutorial -examples. However, they only include brief instructions in a text file -called {\it README}. The examples are located in subdirectories under -the directory \texttt{verification}. Each example is briefly described -below. +The full MITgcm distribution comes with more than a dozen +pre-configured numerical experiments. Some of these example +experiments are tests of individual parts of the model code, but many +are fully fledged numerical simulations. A few of the examples are +used for tutorial documentation in sections \ref{sect:eg-baro} - +\ref{sect:eg-global}. The other examples follow the same general +structure as the tutorial examples. However, they only include brief +instructions in a text file called {\it README}. The examples are +located in subdirectories under the directory \texttt{verification}. +Each example is briefly described below. \subsection{Full list of model examples} @@ -404,15 +403,14 @@ \item \texttt{aim.5l\_LatLon} - Intermediate Atmospheric physics. Global configuration, on latitude longitude grid with 128x64x5 grid - points ($2.8^\circ{\rm degree}$ resolution). + points ($2.8^\circ$ resolution). \item \texttt{adjustment.128x64x1} Barotropic adjustment problem on - latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm - degree}$ resolution). + latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution). \item \texttt{adjustment.cs-32x32x1} Barotropic adjustment problem on - cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm - degree}$ resolution). + cube sphere grid with 32x32 points per face (roughly $2.8^\circ$ + resolution). \item \texttt{advect\_cs} Two-dimensional passive advection test on cube sphere grid. @@ -550,7 +548,7 @@ provide help writing or modifing ``optfiles''. And we encourage users to post new ``optfiles'' (particularly ones for new machines or architectures) to the -\begin{rawhtml} \end{rawhtml} +\begin{rawhtml} \end{rawhtml} MITgcm-support@mitgcm.org \begin{rawhtml} \end{rawhtml} list. @@ -604,6 +602,392 @@ where we are re-directing the stream of text output to the file \texttt{output.txt}. +\subsection{Building/compiling the code elsewhere} + +In the example above (section \ref{sect:buildingCode}) we built the +executable in the {\em input} directory of the experiment for +convenience. You can also configure and compile the code in other +locations, for example on a scratch disk with out having to copy the +entire source tree. The only requirement to do so is you have {\tt + genmake2} in your path or you know the absolute path to {\tt + genmake2}. + +The following sections outline some possible methods of organizing +your source and data. + +\subsubsection{Building from the {\em ../code directory}} + +This is just as simple as building in the {\em input/} directory: +\begin{verbatim} +% cd verification/exp2/code +% ../../../tools/genmake2 +% make depend +% make +\end{verbatim} +However, to run the model the executable ({\em mitgcmuv}) and input +files must be in the same place. If you only have one calculation to make: +\begin{verbatim} +% cd ../input +% cp ../code/mitgcmuv ./ +% ./mitgcmuv > output.txt +\end{verbatim} +or if you will be making multiple runs with the same executable: +\begin{verbatim} +% cd ../ +% cp -r input run1 +% cp code/mitgcmuv run1 +% cd run1 +% ./mitgcmuv > output.txt +\end{verbatim} + +\subsubsection{Building from a new directory} + +Since the {\em input} directory contains input files it is often more +useful to keep {\em input} pristine and build in a new directory +within {\em verification/exp2/}: +\begin{verbatim} +% cd verification/exp2 +% mkdir build +% cd build +% ../../../tools/genmake2 -mods=../code +% make depend +% make +\end{verbatim} +This builds the code exactly as before but this time you need to copy +either the executable or the input files or both in order to run the +model. For example, +\begin{verbatim} +% cp ../input/* ./ +% ./mitgcmuv > output.txt +\end{verbatim} +or if you tend to make multiple runs with the same executable then +running in a new directory each time might be more appropriate: +\begin{verbatim} +% cd ../ +% mkdir run1 +% cp build/mitgcmuv run1/ +% cp input/* run1/ +% cd run1 +% ./mitgcmuv > output.txt +\end{verbatim} + +\subsubsection{Building on a scratch disk} + +Model object files and output data can use up large amounts of disk +space so it is often the case that you will be operating on a large +scratch disk. Assuming the model source is in {\em ~/MITgcm} then the +following commands will build the model in {\em /scratch/exp2-run1}: +\begin{verbatim} +% cd /scratch/exp2-run1 +% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ + -mods=~/MITgcm/verification/exp2/code +% make depend +% make +\end{verbatim} +To run the model here, you'll need the input files: +\begin{verbatim} +% cp ~/MITgcm/verification/exp2/input/* ./ +% ./mitgcmuv > output.txt +\end{verbatim} + +As before, you could build in one directory and make multiple runs of +the one experiment: +\begin{verbatim} +% cd /scratch/exp2 +% mkdir build +% cd build +% ~/MITgcm/tools/genmake2 -rootdir=~/MITgcm \ + -mods=~/MITgcm/verification/exp2/code +% make depend +% make +% cd ../ +% cp -r ~/MITgcm/verification/exp2/input run2 +% cd run2 +% ./mitgcmuv > output.txt +\end{verbatim} + + +\subsection{Using \texttt{genmake2}} +\label{sect:genmake} + +To compile the code, first use the program \texttt{genmake2} (located +in the \texttt{tools} directory) to generate a Makefile. +\texttt{genmake2} is a shell script written to work with all +``sh''--compatible shells including bash v1, bash v2, and Bourne. +Internally, \texttt{genmake2} determines the locations of needed +files, the compiler, compiler options, libraries, and Unix tools. It +relies upon a number of ``optfiles'' located in the +\texttt{tools/build\_options} directory. + +The purpose of the optfiles is to provide all the compilation options +for particular ``platforms'' (where ``platform'' roughly means the +combination of the hardware and the compiler) and code configurations. +Given the combinations of possible compilers and library dependencies +({\it eg.} MPI and NetCDF) there may be numerous optfiles available +for a single machine. The naming scheme for the majority of the +optfiles shipped with the code is +\begin{center} + {\bf OS\_HARDWARE\_COMPILER } +\end{center} +where +\begin{description} +\item[OS] is the name of the operating system (generally the + lower-case output of the {\tt 'uname'} command) +\item[HARDWARE] is a string that describes the CPU type and + corresponds to output from the {\tt 'uname -m'} command: + \begin{description} + \item[ia32] is for ``x86'' machines such as i386, i486, i586, i686, + and athlon + \item[ia64] is for Intel IA64 systems (eg. Itanium, Itanium2) + \item[amd64] is AMD x86\_64 systems + \item[ppc] is for Mac PowerPC systems + \end{description} +\item[COMPILER] is the compiler name (generally, the name of the + FORTRAN executable) +\end{description} + +In many cases, the default optfiles are sufficient and will result in +usable Makefiles. However, for some machines or code configurations, +new ``optfiles'' must be written. To create a new optfile, it is +generally best to start with one of the defaults and modify it to suit +your needs. Like \texttt{genmake2}, the optfiles are all written +using a simple ``sh''--compatible syntax. While nearly all variables +used within \texttt{genmake2} may be specified in the optfiles, the +critical ones that should be defined are: + +\begin{description} +\item[FC] the FORTRAN compiler (executable) to use +\item[DEFINES] the command-line DEFINE options passed to the compiler +\item[CPP] the C pre-processor to use +\item[NOOPTFLAGS] options flags for special files that should not be + optimized +\end{description} + +For example, the optfile for a typical Red Hat Linux machine (``ia32'' +architecture) using the GCC (g77) compiler is +\begin{verbatim} +FC=g77 +DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4' +CPP='cpp -traditional -P' +NOOPTFLAGS='-O0' +# For IEEE, use the "-ffloat-store" option +if test "x$IEEE" = x ; then + FFLAGS='-Wimplicit -Wunused -Wuninitialized' + FOPTIM='-O3 -malign-double -funroll-loops' +else + FFLAGS='-Wimplicit -Wunused -ffloat-store' + FOPTIM='-O0 -malign-double' +fi +\end{verbatim} + +If you write an optfile for an unrepresented machine or compiler, you +are strongly encouraged to submit the optfile to the MITgcm project +for inclusion. Please send the file to the +\begin{rawhtml} \end{rawhtml} +\begin{center} + MITgcm-support@mitgcm.org +\end{center} +\begin{rawhtml} \end{rawhtml} +mailing list. + +In addition to the optfiles, \texttt{genmake2} supports a number of +helpful command-line options. A complete list of these options can be +obtained from: +\begin{verbatim} +% genmake2 -h +\end{verbatim} + +The most important command-line options are: +\begin{description} + +\item[\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} + \end{rawhtml} + \begin{center} + \texttt{MITgcm/tools/build\_options/} + \end{center} + \begin{rawhtml} \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} + \end{rawhtml} + MPICH + \begin{rawhtml} \end{rawhtml} + + \item \begin{rawhtml} + \end{rawhtml} + LAM/MPI + \begin{rawhtml} \end{rawhtml} + + \item \begin{rawhtml} + \end{rawhtml} + MPIexec + \begin{rawhtml} \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} \end{rawhtml}regular + verification runs\begin{rawhtml} \end{rawhtml}) are available + at: + \begin{rawhtml} + \end{rawhtml} + {\footnotesize \tt + http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm\_contrib/test\_scripts/ } + \begin{rawhtml} \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 MITgcm]{Running the model in prognostic mode} \label{sect:runModel} @@ -658,29 +1042,29 @@ written out, which is made of the following files: \begin{itemize} -\item \texttt{U.00000nIter} - zonal component of velocity field (m/s and $> -0 $ eastward). +\item \texttt{U.00000nIter} - zonal component of velocity field (m/s + and positive eastward). -\item \texttt{V.00000nIter} - meridional component of velocity field (m/s -and $> 0$ northward). +\item \texttt{V.00000nIter} - meridional component of velocity field + (m/s and positive northward). -\item \texttt{W.00000nIter} - vertical component of velocity field (ocean: -m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure -i.e. downward). +\item \texttt{W.00000nIter} - vertical component of velocity field + (ocean: m/s and positive upward, atmosphere: Pa/s and positive + towards increasing pressure i.e. downward). -\item \texttt{T.00000nIter} - potential temperature (ocean: $^{0}$C, -atmosphere: $^{0}$K). +\item \texttt{T.00000nIter} - potential temperature (ocean: + $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$). -\item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor -(g/kg). +\item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water + vapor (g/kg). -\item \texttt{Eta.00000nIter} - ocean: surface elevation (m), atmosphere: -surface pressure anomaly (Pa). +\item \texttt{Eta.00000nIter} - ocean: surface elevation (m), + atmosphere: surface pressure anomaly (Pa). \end{itemize} The chain \texttt{00000nIter} consists of ten figures that specify the -iteration number at which the output is written out. For example, \texttt{% -U.0000000300} is the zonal velocity at iteration 300. +iteration number at which the output is written out. For example, +\texttt{U.0000000300} is the zonal velocity at iteration 300. In addition, a ``pickup'' or ``checkpoint'' file called: @@ -717,7 +1101,7 @@ with every netCDF install: \begin{rawhtml} \end{rawhtml} \begin{verbatim} - http://www.unidata.ucar.edu/packages/netcdf/ +http://www.unidata.ucar.edu/packages/netcdf/ \end{verbatim} \begin{rawhtml} \end{rawhtml} and it converts the netCDF binaries into formatted ASCII text files. @@ -726,12 +1110,17 @@ to plot netCDF data and it runs on most OSes: \begin{rawhtml} \end{rawhtml} \begin{verbatim} - http://meteora.ucsd.edu/~pierce/ncview_home_page.html +http://meteora.ucsd.edu/~pierce/ncview_home_page.html \end{verbatim} \begin{rawhtml} \end{rawhtml} \item MatLAB(c) and other common post-processing environments provide various netCDF interfaces including: + \begin{rawhtml} \end{rawhtml} +\begin{verbatim} +http://mexcdf.sourceforge.net/ +\end{verbatim} + \begin{rawhtml} \end{rawhtml} \begin{rawhtml} \end{rawhtml} \begin{verbatim} http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html