| 561 |
output.txt}. |
output.txt}. |
| 562 |
|
|
| 563 |
|
|
|
\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} <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} } |
|
|
|
|
|
|
|
|
|
|
| 564 |
\section[Running MITgcm]{Running the model in prognostic mode} |
\section[Running MITgcm]{Running the model in prognostic mode} |
| 565 |
\label{sect:runModel} |
\label{sect:runModel} |
| 566 |
|
|
Parent Directory
| 
Revision Log
| 
Revision Graph
| 
Patch