Changeset 2206 for trunk/LMDZ.MARS/doc

Timestamp:

Jan 7, 2020, 3:55:33 PM (5 years ago)

Author:

adelavois

Message:

Mars GCM:
Correction of Mars GCM utility:

Variables declaration changed in order to be compiled with ifort (modification of r2204)

Manual User Update:

Old stuff removed from part4: Running the model

File:

• trunk/LMDZ.MARS/doc/run.tex (modified) (5 diffs)

trunk/LMDZ.MARS/doc/run.tex

@@ -94 +94 @@
 
 \section{Installing the model}
-There are two distinct ways of installing/compiling the model:
-One (nowdays depreciated) using scripts in the {\tt LMDZ.MARS}
-directory, and the other (encouraged because one can then also
-run the model on parallel computers) in the {\tt LMDZ.COMMON} directory
-
-\subsection{Settings in LMDZ.MARS (depreciated)}
-\begin{description}
-%\item {\bf -} Copy the basic model directory LMDZ.MARS to your account
-%(the contents of this directory are described in chapter \ref{loc:contenu}).
-
-\item {\bf -} Set some environment variables needed for the compilation
-       of the model (it is also possible to set the environment
-       variables in the {\tt makegcm} script, as explained below):
-  \begin{description}
-  \item {\bf LMDGCM} : Path to the directory where you have put the model
-  (full path).\\
-  If using Csh:
-  \begin{verbatim}
-  setenv  LMDGCM /where/you/put/the/model/LMDZ.MARS
-  \end{verbatim}
-  If using Bash:
-  \begin{verbatim}
-  export  LMDGCM=/where/you/put/the/model/LMDZ.MARS
-  \end{verbatim}  
-  \item {\bf LIBOGCM} : Path to the directory 
-  ({\tt libo} for example) where intermediate objects will be stored
-  during the compilation of the model with the {\tt makegcm} script
-  (if that directory does not
-  exist then {\tt makegcm} will create it).\\
-  If using Csh:
-  \begin{verbatim}
-  setenv  LIBOGCM /where/you/want/objects/to/go/libo
-  \end{verbatim}
-  If using Bash:
-  \begin{verbatim}
-  export  LIBOGCM=/where/you/want/objects/to/go/libo
-  \end{verbatim}
-  \end{description}
-
-\item {\bf -} Knowing where your NetCDF library is installed,
- set environment variables  {\bf NCDFINC} and {\bf NCDFLIB}:
-
-  \begin{description}
-  \item Once the NetCDF library has been compiled (or downloaded),
-  you should have access to the library {\tt libnetcdf.a} itself,
-  the various files ({\tt netcdf.inc}, {\tt netcdf.mod}, ...)
-  to include in programs, and basic NetCDF software ({\it ncdump}
-  and {\it ncgen}).
-
-  \item To ensure that during compilation, the model can find the 
-  NetCDF library and include files,
-  you must declare environment variables {\bf NCDFLIB} and {\bf NCDFINC}
-  (again, it is also possible to set these environment
-      variables in the {\tt makegcm} script, as explained below).
-
-  \item {\bf NCDFLIB} must contain the path to the directory containing
-   the object library {\tt libnetcdf.a}
-   and {\bf NCDFINC} must contain the path to the directory containing
-   the include files ({\tt netcdf.inc},...)\\
-  If using Csh:
-  \begin{verbatim}
-  setenv NCDFINC /wherever/is/netcdf/include
-  setenv NCDFLIB /wherever/is/netcdf/lib
-  \end{verbatim}
-  If using Bash:
-  \begin{verbatim}
-  export NCDFINC=/wherever/is/netcdf/include
-  export NCDFLIB=/wherever/is/netcdf/lib
-  \end{verbatim}
-  \end{description}
-
-\item {\bf -} Go to your {\tt LMDZ.MARS} and adapt the {\tt makegcm}
-  script to fit your needs:
-  \begin{itemize}
-  \item Examples of {\tt makegcm} scripts, adapted for different compilers
-  (pgf90, g95, gfortran and ifort) are provided (files {\tt makegcm},
-  {\tt makegcm\_g95}, {\tt makegcm\_gfortran}, {\tt makegcm\_ifort}) copy or
-  rename the relevant one as {\tt makegcm} in the same directory.
-  \item As mentionned above, you may edit the script to hard code
-  values of {\tt LMDGCM}, {\tt LIBOGCM}, {\tt NCDFINC} and {\tt NCDFLIB} 
-  instead of relying on the use of environment variables (see the commented out
-  examples in the scripts at lignes 20-30). Note that since the {\tt
-  makegcm} is a Csh script, Csh syntax must be used there.
-  \end{itemize}
-
-\end{description}
-
-\subsection{Settings in LMDZ.COMMON (advised)}
+Scripts for installation/compilation for the model are in the {\tt LMDZ.COMMON} directory
+These scripts can also run the model on parallel computers. 
 
 You should first compile the IOIPSL library which is used\footnote{It is in fact for now possible to run the GCM without the IOIPSL library but this requires adding the {\tt -io noioipsl} to the {\tt makelmdz\_fcm} command line, and might no longer be possible in the future.} by the GCM. To do this go to the {\tt LMDZ.COMMON/ioipsl} directory. There are a number of example scripts (depending on machines and compiler suites to use) to run to download and install the ioipsl library. As an illustrative example we detail here using the {\tt install\_ioipsl\_gfortran.bash} script:
@@ -192 +106 @@
 \section{Compiling the model}
 \label{sc:compile}
-\subsection{Compiling in LMDZ.MARS (depreciated)}
-\noindent As explained above, compiling the model is done
-using the {\tt makegcm} script and providing it with the appropriate
-options:
-\begin{itemize}
-\item Example 1: Compiling the Martian model at grid resolution 64x48x25
-for example, type (in compliance with the manual for the makegcm function
-given in section~\ref{sc:compil1})
-
-\begin{verbatim}
-makegcm -d 64x48x25 -p mars gcm
-\end{verbatim}
-
-\noindent
-You will find executable {\bf gcm.e} (the compiled model) in the directory
-where you ran the makegcm command.
-
-%{\bf -} Example 2: Compiling the Martian model with 3 tracers
-%(e.g. CO2, water vapour and ice to simulate the water cycle):
-%\begin{verbatim}
-%makegcm -d 64x48x25 -t 2 -p mars gcm
-%\end{verbatim}
-
-\item Example 2:
-Compiling the the Martian model with your choice of
-compiler options, e.g. to check for array overflow
-(useful for debugging: warning, the model is then much slower!):
-\begin{verbatim}
-makegcm -d 64x48x25 -p mars -O "-C" gcm
-\end{verbatim}
-Note that the {\tt makegcm} script also has a "debug" option which 
-includes a collection of adequate debugging options. To use it,
-simply add the {\tt -debug} option:
-\begin{verbatim}
-makegcm -d 64x48x25 -p mars -debug gcm
-\end{verbatim}
-\end{itemize}
-
-\subsection{Compiling in LMDZ.COMMON (advised)}
 The Bash script {\tt makelmdz\_fcm} is used to compile the model.
 It needs not be modified or adapted to your settings, as all
@@ -243 +118 @@
 with the name used for your own arch files), and multiple options:
 \begin{itemize}
-\item Example 1: Compiling the Martian model at grid resolution 64x48x32
-\begin{verbatim}
-makelmdz_fcm -arch linux-ifort -d 64x48x29 -p mars gcm
-\end{verbatim}
-The executable, {\tt gcm\_64x48x29\_phymars\_seq.e} in the present case,
-will be generated in the {\tt bin} subdirectory.
+\item Example 1: Compiling the Martian model at grid resolution 64x48x49
+\begin{verbatim}
+makelmdz_fcm -arch linux-ifort -d 64x48x49 -p mars gcm
+\end{verbatim}
 \item Example 2: Compiling as above but in "debug" mode
 \begin{verbatim}
-makelmdz_fcm -arch linux-ifort -d 64x48x29 -p mars -debug gcm
+makelmdz_fcm -arch linux-ifort -d 64x48x49 -p mars -debug gcm
 \end{verbatim}
 \item Example 3: Compiling the model to run in parallel (MPI) mode:
 \begin{verbatim}
-makelmdz_fcm -arch linux-ifort -parallel mpi -d 64x48x29 -p mars gcm
-\end{verbatim}
+makelmdz_fcm -arch linux-ifort -parallel mpi -d 64x48x49 -p mars gcm
+\end{verbatim}
+This option is different from the -j option that determines the number of cores when compilation is run in parallel mode.
 \item For an overview of all available options:
 \begin{verbatim}
@@ -323 +197 @@
 \end{verbatim}
 
-
 You might also want to keep all messages and diagnotics written to standard
 output (i.e. the screen). You should then redirect the standard output
@@ -330 +203 @@
 gcm.e > gcm.out 2>&1
 \end{verbatim}
+
+If you want to use parallel mode (as MPI for instance), you should specify it as follow:
+\begin{verbatim}
+mpirun gcm.e > gcm.out 2>&1
+\end{verbatim}
+NB: The definition of parallel parameters, such as number of cores, is dependant on the machine used.
+You should find examples of scripts within other simulations or machine user guides.