Ignore:
Timestamp:
Jul 12, 2011, 7:41:55 PM (13 years ago)
Author:
aslmd
Message:

MESOSCALE: added two new chapters to user manual + figures.

Location:
trunk/MESOSCALE_DEV/MANUAL/SRC
Files:
5 added
5 edited

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  • trunk/MESOSCALE_DEV/MANUAL/SRC/installation.tex

    r214 r218  
    110110tar xzvf LMD_MM_MARS.tar.gz
    111111cd $LMDMOD/LMD_MM_MARS
    112 ./prepare
     112./SRC/SCRIPTS/prepare  ## or simply ./prepare if the script is in LMD_MM_MARS
    113113\end{verbatim}
    114114
    … …  
    137137\end{verbatim}
    138138
    139 \mk
    140 \section{Structure of the \ttt{LMD\_MM\_MARS} directory}
    141 
    142 \sk
    143 Please check the contents of the \ttt{LMD\_MM\_MARS} and the \ttt{LMD\_MM\_MARS/SRC} directories by the following command line:
    144 \begin{verbatim}
    145 ls $MMM
    146 ls $MMM/SRC
    147 \end{verbatim}
    148 
    149 \sk
    150 Contents of~\ttt{LMD\_MM\_MARS} directory:
    151 \begin{citemize}
    152 \item \ttt{makemeso}: this is the \ttt{bash} script to compile the model.
    153 \item \ttt{SRC}: this is a directory containing the model sources.
    154 \item \ttt{SIMU}: this is a directory containing scripts and files for an advanced use.
    155 \item \ttt{WPS_GEOG}: this is a directory containing static data for the model (topography, soil properties, etc...)
    156 \end{citemize}
    157 
    158 \sk
    159 Contents of~\ttt{LMD\_MM\_MARS/SRC} directory:
    160 \begin{citemize}
    161 \item \ttt{WRFV2}: this is a directory containing main model sources (modified WRF dynamics + LMD physics in \ttt{mars_lmd*}).
    162 \item \ttt{PREP\_MARS}: this a directory containing sources for the first preprocessing step.
    163 \item \ttt{WPS}: this a directory containing sources for the second preprocessing step.
    164 \item \ttt{POSTPROC}: this a directory containing postprocessing sources.
    165 \item \ttt{LES} and \ttt{LESnophys_}: these are directories containing sources for Large-Eddy Simulations.
    166 \end{citemize}
    167 
    168 \sk
    169 Contents of~\ttt{LMD\_MM\_MARS} directory:
    170 \begin{citemize}
    171 \item
    172 
    173 \item the sources directory \ttt{SRC};
    174 \item the static data directory \ttt{WPS\_GEOG};
    175 \item the simulation utilities directory \ttt{SIMU}.
    176 \end{citemize}
    177 
    178 
    179 
    180 \sk
    181 Contents of~\ttt{LMD\_MM\_MARS/WPS\_GEOG} directory:
    182 \begin{citemize}
    183 \item three directories \ttt{albedo\_GCM}, \ttt{mola\_GCM}, \ttt{thermal\_GCM}, \ttt{res}
    184 \item one data file \ttt{dust\_tes.nc}
    185 \end{citemize}
    186 
    187 \sk
    188 The directory~\ttt{LMD\_MM\_MARS/SIMU} contains many files and directories not important at this stage. If you used method~$2$, you will probably notice that other directories than~\ttt{LMD\_MM\_MARS} are present in \ttt{\$LMDMOD}, but those are not important at this stage.
    189 
    190 %LMD_MM_MARS/  LMD_MM_MARS_User_Manual.pdf  LMDZ.MARS/  LMDZ.MARS.new
    191 
    192139\clearemptydoublepage

  • trunk/MESOSCALE_DEV/MANUAL/SRC/keep

    r209 r218  
    1 \sk
    2 \marge Now a few environment variables are needed for the model to compile and run correctly.  You also need the environment variable \ttt{\$LMDMOD} to point at the directory where you will install the model.
     1\begin{finger}
     2\item The model presently supports 3 nests, but more nests
     3can be included by adaptating the following files:
     4\begin{verbatim}
     5$LMDMOD/LMD_MM_MARS/SRC/WRFV2/call_meso_inifis3.inc
     6$LMDMOD/LMD_MM_MARS/SRC/WRFV2/call_meso_physiq3.inc
     7$LMDMOD/LMD_MM_MARS/SRC/WRFV2/mars_lmd/libf/duplicate3
     8$LMDMOD/LMD_MM_MARS/SRC/WRFV2/mars_lmd/libf/generate3
     9$LMDMOD/LMD_MM_MARS/SRC/WRFV2/mars_lmd/makegcm*  ## search for 'nest'
     10\end{verbatim}%\pagebreak
     11\end{finger}
    312
    4 \begin{verbatim}       
    5 declare -x LMDMOD=/disk/user/MODELS
    6 \end{verbatim}
    713
    8 \sk
    9 If everything went well up until this stage, you are now ready to install, compile and run the LMD Martian Mesoscale Model.

  • trunk/MESOSCALE_DEV/MANUAL/SRC/user_manual.tex

    r209 r218  
    8686%\newpage
    8787
    88 %\include{foreword}
    89 %\include{whatis}
     88\include{foreword}
     89\include{whatis}
    9090\include{installation}
    91 \include{user_manual_txt}
     91\include{compile_exec}
     92%\include{user_manual_txt}
    9293
    9394\backmatter

  • trunk/MESOSCALE_DEV/MANUAL/SRC/user_manual_txt.tex

    r209 r218  
    11
    2 
    3 
    4 \chapter{Compiling the model and running a test case}
    5 
    6 \vk
    7 This chapter is also meant for first time users of the LMD Martian Mesoscale Model. We describe how to compile the program and run a test case.
    8 
    9 \mk
    10 \subsection{Main compilation step}
    11 \label{sc:makemeso}
    12 
    13 \mk
    14 In order to compile the model, execute the \ttt{makemeso} compilation script
    15 in the \ttt{LMD\_MM\_MARS}\linebreak directory
    16 %
    17 \begin{verbatim}
    18 cd $LMDMOD/LMD_MM_MARS
    19 ./makemeso
    20 \end{verbatim}
    21 %
    22 \marge and answer to the questions about
    23 \begin{asparaenum}[1.]%[\itshape Q1\upshape)]
    24 \item compiler choice (and number of processors if using MPI)
    25 \item number of grid points in longitude [61]
    26 \item number of grid points in latitude [61]
    27 \item number of vertical levels [61]
    28 \item number of tracers [1]
    29 \item number of domains [1]
    30 \end{asparaenum}
    31 
    32 %\mk
    33 \begin{finger}
    34 \item On the first time you compile the model, you will probably wonder what to reply
    35 to questions $2$ to $6$ \ldots type the answers given in brackets to compile an executable suitable
    36 for the test case given below.
    37 \item Suppose you compiled a version of the model for a given set of parameters $1$ to $6$
    38 to run a specific compilation.
    39 If you would like to run another simulation
    40 with at least one of parameters $1$ to $6$
    41 subject to change, the model needs to be recompiled\footnote{This
    42 necessary recompilation each time the number of grid points,
    43 tracers and domains is modified is imposed by the LMD physics code.
    44 The WRF dynamical core alone is much more flexible.} with \ttt{makemeso}.
    45 \item When you use parallel computations, please bear in mind that with
    46 $2$ (resp. $4$, $6$, $8$, $16$) processors the whole domain would be separated
    47 into $2$ (resp. $2$, $3$, $4$, $4$) tiles over
    48 the latitude direction and $1$ (resp. $2$, $2$, $2$, $4$) tile over the longitude direction.
    49 Thus make sure that the number of grid points minus $1$ in each direction
    50 could be divided by the aforementioned number of tiles over the considered
    51 direction.
    52 \item If you use grid nesting, note that no more than $4$ processors can be used.
    53 \end{finger}
    54 
    55 \mk
    56 \marge The \ttt{makemeso} is an automated script which performs
    57 the following serie of tasks:
    58 %It is useful to detail and comment the  performed by the \ttt{makemeso} script:
    59 \begin{citemize}
    60 \item determine if the machine is 32 or 64 bits;
    61 \item ask the user about the compilation settings;
    62 \item create a corresponding directory \ttt{\$LMDMOD/LMD\_MM\_MARS/DIRCOMP};
    63 \begin{finger}
    64 \item For example, a \ttt{DIRCOMP} directory named \ttt{g95\_32\_single}
    65 is created if the user requested
    66 a \ttt{g95} compilation of the code for single-domain simulations
    67 on a 32bits machine.
    68 \end{finger}
    69 \item generate with \ttt{copy\_model} a directory \ttt{DIRCOMP/WRFV2} containing links to \ttt{SRC/WRFV2} sources;
    70 \begin{finger}
    71 \item This method ensures that any change to the model sources would
    72 be propagated to all the different \ttt{DIRCOMP} installation folders.
    73 \end{finger}
    74 \item execute the WRF \ttt{configure} script with the correct option;
    75 \item tweak the resulting \ttt{configure.wrf} file to include a link towards the Martian physics;
    76 \item calculate the total number of horizontal grid points handled by the LMD physics;
    77 \item duplicate LMD physical sources if nesting is activated;
    78 \begin{finger}
    79 \item The model presently supports 3 nests, but more nests
    80 can be included by adaptating the following files:
    81 \begin{verbatim}
    82 $LMDMOD/LMD_MM_MARS/SRC/WRFV2/call_meso_inifis3.inc
    83 $LMDMOD/LMD_MM_MARS/SRC/WRFV2/call_meso_physiq3.inc
    84 $LMDMOD/LMD_MM_MARS/SRC/WRFV2/mars_lmd/libf/duplicate3
    85 $LMDMOD/LMD_MM_MARS/SRC/WRFV2/mars_lmd/libf/generate3
    86 $LMDMOD/LMD_MM_MARS/SRC/WRFV2/mars_lmd/makegcm*  ## search for 'nest'
    87 \end{verbatim}%\pagebreak
    88 \end{finger}
    89 \item compile the LMD physical packages with the appropriate \ttt{makegcm} command
    90 and collect the compiled objects in the library \ttt{liblmd.a};
    91 \begin{finger}
    92 \item During this step that could be a bit long,
    93 especially if you defined more than one domain,
    94 the \ttt{makemeso} script provides you with the full path towards
    95 the text file \ttt{log\_compile\_phys} in which you can check for
    96 compilation progress and possible errors.
    97 %
    98 In the end of the process, you will find an
    99 error message associated to the generation of the
    100 final executable.
    101 %
    102 Please do not pay attention to this, as the compilation of the LMD
    103 sources is meant to generate a library of
    104 compiled objects called \ttt{liblmd.a} instead of a program.
    105 \end{finger}
    106 \item compile the modified Martian ARW-WRF solver, including
    107 the \ttt{liblmd.a} library;
    108 \begin{finger}
    109 \item When it is the first time the model is compiled, this
    110 step could be quite long.
    111 %
    112 The \ttt{makemeso} script provides you with a \ttt{log\_compile}
    113 text file where the progress of the compilation can be checked
    114 and a \ttt{log\_error} text file listing errors and warnings
    115 during compilation.
    116 %
    117 A list of warnings related to \ttt{grib}
    118 utilities (not used in the Martian model)
    119 may appear and have no impact on the
    120 final executables.
    121 \item The compilation with \ttt{g95} might be unsuccessful
    122 due to some problems with files related to terrestrial microphysics.
    123 %
    124 Please type the following commands:
    125 \begin{verbatim}
    126 cd $LMDMOD/LMD_MM_MARS/SRC
    127 tar xzvf g95.tar.gz
    128 cp -f g95/WRFV2_g95_fix/* WRFV2/phys/
    129 cd $LMDMOD/LMD_MM_MARS
    130 \end{verbatim}
    131 \marge then recompile the model with the \ttt{makemeso} command.
    132 \end{finger}
    133 \item change the name of the executables in agreements with the
    134 settings provided by the user.
    135 \begin{finger}
    136 \item If you choose to answer to the \ttt{makemeso} questions using the
    137 aforementioned parameters in brackets, you should have in the
    138 \ttt{DIRCOMP} directory two executables:
    139 \begin{verbatim}
    140 real_x61_y61_z61_d1_t1_p1.exe
    141 wrf_x61_y61_z61_d1_t1_p1.exe
    142 \end{verbatim}
    143 %
    144 The directory also contains a text file
    145 in which the answers to the questions are stored, which
    146 allows you to re-run the script without the
    147 ``questions to the user" step:
    148 \begin{verbatim}
    149 ./makemeso < makemeso_x61_y61_z61_d1_t1_p1
    150 \end{verbatim}
    151 \end{finger}
    152 \end{citemize}
    153 
    154 \mk
    155 \section{Running a simple test case}
    156 \label{sc:arsia}
    157 
    158 \mk
    159 We suppose that you had successfully compiled
    160 the model at the end of the previous section
    161 and you had used the answers in brackets
    162 to the \ttt{makemeso} questions.
    163 
    164 \mk
    165 \marge In order to test the compiled executables,
    166 a ready-to-use test case
    167 (with pre-generated initial and boundary
    168 conditions) is proposed
    169 in the \ttt{LMD\_MM\_MARS\_TESTCASE.tar.gz}
    170 archive you can download at
    171 \url{http://www.lmd.jussieu.fr/~aslmd/LMD_MM_MARS/LMD_MM_MARS_TESTCASE.tar.gz}.
    172 %
    173 This test case simulates the hydrostatic
    174 atmospheric flow around Arsia Mons during half a sol
    175 with constant thermal inertia, albedo
    176 and dust opacity.
    177 
    178 \begin{finger}
    179 \item Though the simulation reproduces some reasonable
    180 features of the mesoscale circulation around Arsia
    181 Mons (e.g. slope winds), it should not be used
    182 for scientific purpose, for the number of grid points
    183 is unsufficient for single-domain simulation
    184 and the integration time is below the necessary spin-up time.
    185 \end{finger}
    186 %\pagebreak
    187 
    188 \marge To launch the test simulation, please type
    189 the following commands, replacing the
    190 \ttt{g95\_32\_single} directory with its corresponding
    191 value on your system:
    192 %
    193 \begin{verbatim}
    194 cp LMD_MM_MARS_TESTCASE.tar.gz $LMDMOD/LMD_MM_MARS/
    195 tar xzvf LMD_MM_MARS_TESTCASE.tar.gz
    196 cd TESTCASE
    197 ln -sf ../g95_32_single/real_x61_y61_z61_d1_t1_p1.exe wrf.exe 
    198 nohup wrf.exe > log_wrf &
    199 \end{verbatim}
    200 
    201 %tar xzvf wrfinput.tar.gz
    202 
    203 \begin{finger}
    204 \item If you compiled the model using MPICH2,
    205 the command to launch a simulation is slightly different:
    206 %
    207 \begin{verbatim}
    208 [simulation on 2 processors on 1 machine]
    209 mpd &      # first-time only (or after a reboot)
    210            # NB: may request the creation of a file .mpd.conf
    211 mpirun -np 8 wrf.exe < /dev/null &      # NB: mpirun is only a link to mpiexec 
    212 tail -20 rsl.out.000?     # to check the outputs
    213 \end{verbatim}
    214 \begin{verbatim}
    215 [simulation on 16 processors in 4 connected machines]
    216 echo barry.lmd.jussieu.fr > ~/mpd.hosts
    217 echo white.lmd.jussieu.fr >> ~/mpd.hosts
    218 echo loves.lmd.jussieu.fr >> ~/mpd.hosts
    219 echo tapas.lmd.jussieu.fr >> ~/mpd.hosts
    220 ssh barry.lmd.jussieu.fr   # make sure that ssh to other machines
    221                            # is possible without authentification
    222 mpdboot -f ~/mpd.hosts -n 4
    223 mpdtrace
    224 mpirun -l -np 16 wrf.exe < /dev/null &   # NB: mpirun is only a link to mpiexec
    225 tail -20 rsl.out.00??     # to check the outputs
    226 \end{verbatim}
    227 \end{finger}
    2282
    2293
    … …  
    829603
    830604\mk
    831 \section{Postprocessing utilities and graphics}
     605\section{Postprocessing utilities and graphics}\label{postproc}
    832606
    833607\begin{remarque}

  • trunk/MESOSCALE_DEV/MANUAL/SRC/whatis.tex

    r209 r218  
    22
    33\vk
    4 This chapter comprises the excerpts from \textit{Spiga and Forget} [2009]\nocite{Spig:09} dedicated to a general scientific and technical description of the LMD Martian Mesoscale Model, of its design and capabilities. Further details can be found in the reference paper \textit{Spiga and Forget} [2009]\nocite{Spig:09} and subsequent papers about mesoscale applications: e.g., \textit{Spiga and Lewis} [2010]\nocite{Spig:10dust} and \textit{Spiga et al.} [2011]\nocite{Spig:11ti}. An introduction to Large-Eddy Simulations can be found in \textit{Spiga et al.} [2010]\nocite{Spig:10bl}. The figure at the end of this chapter summarizes the main points detailed in this introduction.
     4This chapter comprises the excerpts from \textit{Spiga and Forget} [2009]\nocite{Spig:09} dedicated to a general scientific and technical description of the LMD Martian Mesoscale Model, of its design and capabilities. Further details can be found in the reference paper \textit{Spiga and Forget} [2009]\nocite{Spig:09} and subsequent papers about mesoscale applications: e.g., \textit{Spiga and Lewis} [2010]\nocite{Spig:10dust} and \textit{Spiga et al.} [2011]\nocite{Spig:11ti}. An introduction to Large-Eddy Simulations can be found in \textit{Spiga et al.} [2010]\nocite{Spig:10bl}. Figure~\ref{modelstructure} summarizes the main points detailed in this introduction.
     5
     6\begin{center}
     7\begin{figure}[p]
     8\includegraphics[width=0.99\textwidth]{meso.pdf}
     9\caption{\label{modelstructure} An illustration of the LMD Martian Mesoscale Model design and capabilities.}
     10\end{figure}
     11\end{center}
    512
    613\mk
    … …  
    133140The initial atmospheric state obtained through this ``hybrid" method ensures low-amplitude adjustments of the meteorological fields by the mesoscale model at the beginning of the performed simulations (i.e., in the first thousands of seconds). Furthermore, the continuity between the large-scale forcing and the mesoscale computations near the limits of the domain, as well as the numerical stability of the simulations, appear as significantly improved compared to methods either based on extrapolation (especially in areas of uneven terrains) or terrain-following interpolation.
    134141
    135 %\pagebreak
    136 \includepdf[pages=1,offset=25mm -20mm]{meso.pdf}
     142%\includepdf[pages=1,offset=25mm -20mm]{meso.pdf}
    137143\clearemptydoublepage
    138144
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