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Timestamp:
Jan 8, 2012, 10:57:06 PM (13 years ago)
Author:
aslmd
Message:

MESOSCALE: final version of the user manual

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

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    10 The compilation operations indicated here need to be done only once on a given system.
     10The compilation operations indicated here need to be done only once on a given system with a given compiler.
    1111
    1212\sk
    … …  
    3030ln -sf ../SRC/SCRIPTS/prepare_ini .
    3131./prepare_ini
    32 echo $PWD
    33 \end{verbatim}
     32\end{verbatim}
     33%%echo $PWD
    3434
    3535\sk
    … …  
    3737
    3838\sk
    39 The script \ttt{prepare\_ini} plays for the preprocessing tools a similar role as the \ttt{copy\_model} with the model sources: files are simply linked to their actual location in the \ttt{SRC} folder. Once you have executed \ttt{prepare\_ini}, please check that two folders were generated: \ttt{PREP\_MARS} and \ttt{WPS}. In the \ttt{PREP\_MARS} directory, please compile the programs \ttt{create\_readmeteo.exe} and \ttt{readmeteo.exe}, using the compiler mentioned in the name of the current installation directory. In the \ttt{WPS} directory, please compile the programs \ttt{geogrid.exe} and \ttt{metgrid.exe}. Here are the useful commands:
     39The script \ttt{prepare\_ini} plays for the preprocessing tools a similar role as the script \ttt{copy\_model} for the model sources: files are simply linked to their actual location in the \ttt{SRC} folder. Once you have executed \ttt{prepare\_ini}, please check that two folders were generated: \ttt{PREP\_MARS} and \ttt{WPS}. In the \ttt{PREP\_MARS} directory, please compile the programs \ttt{create\_readmeteo.exe} and \ttt{readmeteo.exe}, using the compiler mentioned in the name of the current installation directory. In the \ttt{WPS} directory, please compile the programs \ttt{geogrid.exe} and \ttt{metgrid.exe}. Here are the useful commands:
    4040
    4141\begin{verbatim}
    … …  
    5151
    5252\sk
    53 Apart from the executables just compiled, the preprocessing utilities include \ttt{real.exe}, which was compiled by the \ttt{makemeso} script along with the mesoscale model executable \ttt{wrf.exe}\footnote{Even though the name of the executable reads e.g. \ttt{real\_x61\_y61\_z61\_d1\_t1\_p1.exe}, such program is not related to the specific \ttt{makemeso} parameters -- contrary to the \ttt{wrf.exe} executable. We just found that renaming the (possibly similar if the model sources were not modified) \ttt{real.exe} executable was a practical way not to confuse between executables compiled at different moments.}. \ttt{real.exe} should be copied or linked in the simulation directory (e.g. \ttt{TESTCASE} for the Arsia Mons test case) to be at the same level than \ttt{namelist.input}.
     53Apart from the executables just compiled, the preprocessing utilities include \ttt{real.exe}, which was compiled by the \ttt{makemeso} script along with the mesoscale model executable \ttt{wrf.exe}\footnote{Even though the name of the executable reads e.g. \ttt{real\_x61\_y61\_z61\_d1\_t1\_p1.exe}, such program is not related to the specific \ttt{makemeso} parameters -- contrary to the \ttt{wrf.exe} executable. We just found that renaming the (possibly similar if the model sources were not modified) \ttt{real.exe} executable was a practical way not to confuse between executables compiled at different moments.} (cf. chapter~\ref{compile}). \ttt{real.exe} should be copied or linked in the simulation directory (e.g. \ttt{TESTCASE} for the Arsia Mons test case) to be at the same level than \ttt{namelist.input}.
    5454
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    … …  
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    88 The other necessary operation to prepare the LMD-MGCM for step~1 is to store a set of initial states for the LMD-MGCM to start with, based on previous typical LMD-MGCM runs having reached equilibrium after ten years of integration. A reference database can be found in the following online archive~\url{ftp://ftp.lmd.jussieu.fr/pub/aslmd/STARTBASE_64_48_32_t2.tar.gz}. This archive must be extracted somewhere on a disk that would be accessible to the system you plan to run the mesoscale model on. A link named~\ttt{startbase} towards the \ttt{STARTBASE\_64\_48\_32\_t2} directory must be created in the directory~\ttt{\$MESO/LMDZ.MARS/myGCM}. If those operations went well, please try the command line~\ttt{echo 22 | launch\_gcm} in this directory, which should launch the GCM integrations on your system.
     88The other necessary operation to prepare the LMD-MGCM for step~1 is to store a set of initial states for the LMD-MGCM to start with, based on previous typical LMD-MGCM runs having reached equilibrium after ten years of integration. A reference database\footnote{If another database is used, \ttt{compile} must be edited; default is~$64 \times 48 \times 32$ GCM runs with~$2$ tracers.} can be found in the following online archive~\url{ftp://ftp.lmd.jussieu.fr/pub/aslmd/STARTBASE_64_48_32_t2.tar.gz}. This archive must be extracted somewhere on a disk that would be accessible to the system you plan to run the mesoscale model on. A link named~\ttt{startbase} towards the \ttt{STARTBASE\_64\_48\_32\_t2} directory must be created in the directory~\ttt{\$MESO/LMDZ.MARS/myGCM}.
     89
     90\sk
     91GCM integrations can then be launched in~\ttt{\$MESO/LMDZ.MARS/myGCM} using~\ttt{launch\_gcm}.
    8992
    9093\mk
    … …  
    98101\begin{finger}
    99102\item changing the season of simulation implies to re-run the LMD Mars GCM for this specific season to prepare initial and boundary conditions for the mesoscale model. Hence e.g. \ttt{start\_month} is labelled with \ttt{(p1)} because changing this in \ttt{namelist.input} requires a complete reprocessing from step~$1$ to step~$3$ to successfully launch the simulation.
    100 \item changing the number of horizontal grid points for the mesoscale domain implies to interpolate the static and GCM fields to the new domain, while no new computations on the GCM side are needed. Hence e.g. \ttt{e\_we} is labelled with \ttt{(p2)} because changing this in \ttt{namelist.input} requires a reprocessing from step~$2$ to step~$3$ to successfully launch the simulation (and also for this specific parameter recompiling with \ttt{makemeso} is needed).
     103\item changing the number of horizontal grid points for the mesoscale domain implies to interpolate the static and GCM fields to the new domain, while no new computations on the GCM side are needed. Hence e.g. \ttt{e\_we} is labelled with \ttt{(p2)} because changing this in \ttt{namelist.input} requires a reprocessing from step~$2$ to step~$3$ to successfully launch the simulation (for this specific parameter recompiling with \ttt{makemeso} is also needed).
    101104\item changing the position of model top implies to interpolate initial and boundary conditions to the new vertical levels, while no horizontal re-interpolations are needed. Hence e.g. \ttt{p\_top\_requested} is labelled with \ttt{(p3)} because changing this requires a reprocessing of step~$3$.
    102105\item changing the timestep for dynamical integration does not require any change in initial and boundary conditions. Hence e.g. \ttt{time\_step} is not labelled with \ttt{(p1)}, \ttt{(p2)} or \ttt{(p3)}.
    … …  
    114117
    115118\sk
    116 Here we assume that the user has chosen a given Martian sol or $L_s$ on which to start the mesoscale simulation. As already mentionned in section~\ref{namelist}, the file \ttt{\$MMM/SIMU/calendar} reproduced in appendix can help with this choice (i.e. sol$\rightarrow$$L_s$$\rightarrow$mesoscale date and vice-versa). In addition, the user has to check in the \ttt{calendar} file which sol is before the one wanted for simulation start and has $99$ in the first column: such sols are the ones for which an initial starting file for the GCM is available. Then the number of GCM simulated days \ttt{nday} in \ttt{\$MESO/LMDZ.MARS/myGCM/run.def} must be set accordingly: suppose you want to start a mesoscale simulation at sol~9 during 4~sols, then according to the \ttt{calendar} file, sol~8 is the closest file before sol~9 to be in the database, so \ttt{nday} must be at least~$5$. For optimal forcing at the boundaries, we advise you to write the meteorological fields to the \ttt{diagfi.nc} file at least each two hours, or ideally each hour, i.e. \ttt{ecritphy} is respectively~$80$ or~$40$ in \ttt{\$MESO/LMDZ.MARS/myGCM/run.def}. Eventually the GCM run can be launched using the following commands and should produce a netCDF data file named \ttt{diagfi.nc}:
     119Here we assume that the user has chosen a given Martian sol or $L_s$ on which to start the mesoscale simulation. As already mentionned in section~\ref{namelist}, the file \ttt{\$MMM/SIMU/calendar} reproduced in appendix can help with this choice (i.e. sol$\rightarrow$$L_s$$\rightarrow$mesoscale date and vice-versa). In addition, the user has to check in the \ttt{calendar} file which sol is before the one wanted for simulation start and has $99$ in the first column: such sols are the ones for which an initial starting file for the GCM is available. Then the number of GCM simulated days \ttt{nday} in \ttt{\$MESO/LMDZ.MARS/myGCM/run.def} must be set accordingly: suppose you want to start a mesoscale simulation at sol~9 during 4~sols, then according to the \ttt{calendar} file, sol~8 is the closest file before sol~9 to be in the database, so \ttt{nday} must be at least~$5$. For optimal forcing at the boundaries, we advise you to write the meteorological fields to the \ttt{diagfi.nc} file at least each two hours, or ideally each hour\footnote{The parameter \ttt{interval\_seconds} in \ttt{namelist.wps} (see section~\ref{wps}) has to be set accordingly.}, i.e. \ttt{ecritphy} is respectively~$80$ or~$40$ in \ttt{\$MESO/LMDZ.MARS/myGCM/run.def}. Eventually the GCM run can be launched using the following commands and should produce a netCDF data file named \ttt{diagfi.nc}:
    117120
    118121\begin{verbatim}
    … …  
    134137
    135138\sk
    136 Once the GCM simulations are finished, programs in the \ttt{PREP\_MARS} directory allow the user to convert the data\footnote{If the fields \ttt{emis}, \ttt{co2ice}, \ttt{q01}, \ttt{q02}, \ttt{tsoil} are missing in the \ttt{diagfi.nc} file, those are replaced by respective default values $0.95$, $0$, $0$, $0$, tsurf.} from the NETCDF \ttt{diagfi.nc} file into separated binary datafiles for each date contained in \ttt{diagfi.nc}, which follows the formatting needed by the preprocessing programs at step 2. These programs can be executed by the following commands; if everything went well with the conversion, the directory \ttt{\$MESO/TMPDIR/WPSFEED} should contain files named \ttt{LMD:*}.
    137 
    138 \begin{verbatim}
    139 cd $MMM/your_install_dir/PREP\_MARS
     139Once the GCM simulations are finished, programs in the \ttt{PREP\_MARS} directory allow the user to convert the data from the NETCDF \ttt{diagfi.nc} file into separated binary datafiles\footnote{If the fields \ttt{emis}, \ttt{co2ice}, \ttt{q01}, \ttt{q02}, \ttt{tsoil} are missing in the \ttt{diagfi.nc} file, those are replaced by respective default values $0.95$, $0$, $0$, $0$, tsurf.} for each date contained in \ttt{diagfi.nc} and formatted for the preprocessing programs at step 2. These programs can be executed by the following commands; if everything went well with the conversion, the directory \ttt{\$MESO/TMPDIR/WPSFEED} should contain files named \ttt{LMD:*}.
     140
     141\begin{verbatim}
     142cd $MMM/your_install_dir/PREP_MARS
    140143echo 1 | ./create_readmeteo.exe     # drop the "echo 1 |" if you want control
    141144./readmeteo.exe < readmeteo.def
    … …  
    154157\end{verbatim}
    155158
    156 The result of \ttt{geogrid.exe} -- and thus the definition of the mesoscale domain -- can be checked in the NETCDF file \ttt{geo\_em.d01.nc} (using for instance \ttt{ncview}, or your favorite graphical interface for netCDF files, or python-based scripts as in section~\ref{postproc}). If you are unhappy with the results or you want to change the location of the mesoscale domain on the planet, the horizontal resolution, the number of grid points \ldots, please modify the parameter file \ttt{namelist.wps}, content thereof is reproduced/commented on the next page, and execute again \ttt{geogrid.exe}.
    157 
    158 \begin{finger}
    159 \item No input meteorological data are actually needed to execute \ttt{geogrid.exe}. This step~2a can be achieved/prepared e.g. before step~1. It is probably a good idea to prepare step~2 by choosing the mesoscale simulation domain while GCM computations being performed done during step~1.
     159The result of \ttt{geogrid.exe} -- and thus the definition of the mesoscale domain -- can be checked in the NETCDF file \ttt{geo\_em.d01.nc} (using for instance \ttt{ncview}, or your favorite graphical interface for netCDF files, or python-based scripts as in section~\ref{postproc}). If you are unhappy with the results or you want to change the location of the mesoscale domain on the planet, the horizontal resolution, the number of grid points \ldots, please modify the parameter file \ttt{namelist.wps}, content thereof is reproduced/commented on the next page\footnote{You may find the corresponding file in \ttt{\$MMM/SIMU/namelist.wps\_example}.}, and execute again \ttt{geogrid.exe}.
     160
     161\begin{finger}
     162\item No input meteorological data are actually needed to execute \ttt{geogrid.exe}. This step~2a can be done e.g. before step~1. It is probably a good idea to prepare step~2 by choosing the mesoscale simulation domain while GCM computations being performed during step~1.
    160163\item More details about the database and more options of interpolation could be found in the file \ttt{geogrid/GEOGRID.TBL} (for advanced users only).
    161164\item Two examples of \ttt{namelist.wps} parameters are given in Figure~\ref{vallespolar} with resulting domains.
    … …  
    163166
    164167\footnotesize
    165 \codesource{namelist.wps_TEST}
     168\codesource{namelist.wps_example}
    166169\normalsize
    167170
    … …  
    185188
    186189\sk
    187 \paragraph{Step 2b} Once the \ttt{geo\_em} file(s) are generated, the \ttt{metgrid.exe} program performs a similar horizontal interpolation of the meteorological fields to the mesoscale domain as the one performed by \ttt{geogrid.exe} for the surface data (interpolation options can be modified by advanced users in \ttt{metgrid/METGRID.TBL}). Then the program writes the results in \ttt{met\_em} files and also collects the static fields and domain parameters included in the \ttt{geo\_em} file(s). If everything went well with the commands below, the directory \ttt{\$MESO/TMPDIR/WRFFEED} should contain \ttt{met\_em.*} files.
     190\paragraph{Step 2b} Once the \ttt{geo\_em} file(s) are generated, the \ttt{metgrid.exe} program performs a similar horizontal interpolation of the meteorological fields to the mesoscale domain as the one performed by \ttt{geogrid.exe} for the surface data (interpolation options can be modified by advanced users in \ttt{metgrid/METGRID.TBL}). Then the program writes the results in \ttt{met\_em} files and also collects the static fields and domain parameters included in the \ttt{geo\_em} file(s). If everything went well with the commands below, the directory \ttt{\$MESO/TMPDIR/WRFFEED/current} should contain \ttt{met\_em.*} files.
    188191
    189192\begin{verbatim}
    … …  
    197200
    198201\sk
    199 The last preprocessing step before being able to run the mesoscale simulation at step~4 is to execute \ttt{real.exe} to perform the interpolation from the vertical levels of the GCM to the vertical levels defined in the mesoscale model. This program also prepares the final initial state for the simulation in files called \ttt{wrfinput} and the boundary conditions in files called \ttt{wrfbdy}. To successfully execute \ttt{real.exe}, you need the \ttt{met\_em.*} files and the \ttt{namelist.input} file to be in the same directory as \ttt{real.exe}. Parameters in \ttt{namelist.input} which controls the behavior of the vertical interpolation are those labelled with \ttt{(p3)} in the detailed list introduced in chapter~\ref{zeparam}.
     202The last preprocessing step before being able to run the mesoscale simulation at step~4 is to execute \ttt{real.exe} to perform the interpolation from the vertical levels of the GCM to the vertical levels defined in the mesoscale model. This program also prepares the final initial state for the simulation in files named \ttt{wrfinput} and the boundary conditions in files named \ttt{wrfbdy}. To successfully execute \ttt{real.exe}, you need the \ttt{met\_em.*} files and the \ttt{namelist.input} file to be in the same directory as \ttt{real.exe}. Parameters in \ttt{namelist.input} which controls the behavior of the vertical interpolation are those labelled with \ttt{(p3)} in the detailed list introduced in chapter~\ref{zeparam}.
    200203
    201204\begin{verbatim}
    202205cd $MMM/TESTCASE   ## or anywhere you would like to run the simulation
    203 ln -sf $MESO/TMPDIR/WRFFEED/met_em* .
     206ln -sf $MESO/TMPDIR/WRFFEED/current/met_em* .
    204207./real.exe
    205208\end{verbatim}
    206209
    207210\sk
    208 The final message of the \ttt{real.exe} should claim the success of the processes and you are now ready to launch the integrations of the LMD Martian Mesoscale Model again with the \ttt{wrf.exe} command as in section \ref{sc:arsia}.
    209 
    210 \sk
    211 \begin{finger}
    212 \item \textbf{ When you modify either \ttt{namelist.wps} or \ttt{namelist.input}, make sure that the common parameters are exactly similar in both files (especially when running nested simulations) otherwise either \ttt{real.exe} or \ttt{wrf.exe} command will exit with an error message. Also, obviously the dates sent to \ttt{launch\_gcm} and written in both \ttt{namelist.input} and \ttt{namelist.wps} should be consistent. }
     211The final message of the \ttt{real.exe} should claim the success of the processes and you are now ready to launch the integrations of the LMD Martian Mesoscale Model with the \ttt{wrf.exe} command as in section \ref{sc:arsia}.
     212
     213\sk
     214\begin{finger}
     215\item \textbf{ When you modify either \ttt{namelist.wps} or \ttt{namelist.input}, make sure that the common parameters are exactly similar in both files (especially when running nested simulations) otherwise either \ttt{real.exe} or \ttt{wrf.exe} command will exit with an error message. Obviously the dates sent to \ttt{launch\_gcm} and set in both \ttt{namelist.input} and \ttt{namelist.wps} should be consistent too. }
    213216\end{finger}
    214217
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