Difference between revisions of "Tool Box"

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(→‎Continuing Simulations)
(→‎bash scripts)
Line 55: Line 55:
  
 
<syntaxhighlight lang="bash">
 
<syntaxhighlight lang="bash">
−
ok
+
#!/bin/bash
 +
###########################################################################
 +
# Script to perform several chained LMD Mars GCM simulations
 +
# SET HERE the maximum total number of simulations
 +
 
 +
nummax=200
 +
 
 +
###########################################################################
 +
 
 +
 
 +
echo "---------------------------------------------------------"
 +
echo "STARTING LOOP RUN"
 +
echo "---------------------------------------------------------"
 +
 
 +
dir=`pwd`
 +
machine=`hostname`
 +
address=`whoami`
 +
 
 +
# Look for file "num_run" which should contain
 +
# the value of the previously computed season
 +
# (defaults to 0 if file "num_run" does not exist)
 +
if [[ -r num_run ]] ; then
 +
  echo "found file num_run"
 +
  numold=`cat num_run`
 +
else
 +
  numold=0
 +
fi
 +
echo "numold is set to" ${numold}
 +
 
 +
 
 +
# Set value of current season
 +
(( numnew = ${numold} + 1 ))
 +
echo "numnew is set to" ${numnew}
 +
 
 +
# Look for initialization data files (exit if none found)
 +
if [[ ( -r start${numold}.nc  &&  -r startfi${numold}.nc ) ]] ; then
 +
  \cp -f start${numold}.nc start.nc
 +
  \cp -f startfi${numold}.nc startfi.nc
 +
else
 +
  if (( ${numold} == 99999 )) ; then
 +
    echo "No run because previous run crashed ! (99999 in num_run)"
 +
    exit
 +
  else
 +
  echo "Where is file start"${numold}".nc??"
 +
  exit
 +
  fi
 +
fi
 +
 
 +
# Run GCM
 +
mpirun -np 4 gcm_64x48x26_phystd_para.e < diagfi.def > lrun${numnew}
 +
 
 +
 
 +
# Check if run ended normaly and copy datafiles
 +
if [[ ( -r restartfi.nc  &&  -r restart.nc ) ]] ; then
 +
  echo "Run seems to have ended normaly"
 +
 
 +
 
 +
  \mv -f restart.nc start${numnew}.nc
 +
  \mv -f restartfi.nc startfi${numnew}.nc 
 +
   
 +
else
 +
  if [[ -r num_run ]] ; then
 +
    \mv -f num_run num_run.crash
 +
  else
 +
    echo "No file num_run to build num_run.crash from !!"
 +
    # Impose a default value of 0 for num_run
 +
    echo 0 > num_run.crash
 +
  fi
 +
echo 99999 > num_run
 +
############## To receive an Email message if the run crashes ########
 +
mail -s "crash run GCM" $address <<ENDMAIL
 +
The run on $machine in $dir has just crashed.
 +
ENDMAIL
 +
############################################""
 +
exit
 +
fi
 +
 
 +
# Copy other datafiles that may have been generated
 +
if [[ -r diagfi.nc ]] ; then
 +
  \mv -f diagfi.nc diagfi${numnew}.nc
 +
fi
 +
if [[ -r diagsoil.nc ]] ; then
 +
  \mv -f diagsoil.nc diagsoil${numnew}.nc
 +
fi
 +
if [[ -r stats.nc ]] ; then
 +
  \mv -f stats.nc stats${numnew}.nc
 +
fi
 +
if [[ -f profiles.dat ]] ; then
 +
  \mv -f profiles.dat profiles${numnew}.dat
 +
  \mv -f profiles.hdr profiles${numnew}.hdr
 +
fi
 +
 
 +
# Prepare things for upcoming runs by writing
 +
# value of computed season in file num_run
 +
echo ${numnew} > num_run
 +
 
 +
# If we are over nummax : stop
 +
if (( $numnew + 1 > $nummax )) ; then
 +
  exit
 +
else
 +
  \cp -f run_gnome exe_mars
 +
  ./exe_mars
 +
fi
 +
 
 +
 
 
</syntaxhighlight>
 
</syntaxhighlight>
  

Revision as of 09:22, 11 May 2022

Pre-processing Tools

newstart

start2archive

visualization tools

other third party scripts and tools

TO BE COMPLETED

Post-processing tools

zrecast

TO BE COMPLETED

mass stream function

The mass stream function (and the total angular momentum) can be computed from a diagfi.nc or a stats.nc, using the streamfunction.F90 script. The script is located at 

trunk/LMDZ.GENERIC/utilities

To compile the script, open the compile file in the same directory and do the following:

  • Replace "pgf90" with your favorite fortran compiler
  • replace "/distrib/local/netcdf/pgi_7.1-6_32/lib" with the lib address and directory that contains your NetCDF library (file libnetcdf.a).
  • Replace "/distrib/local/netcdf/pgi_7.1-6_32/include" with the address of the directory that contains the NetCDF include file (netcdf.inc).
  • You can mess with the compiling options but it is not mandatory.

Once the script is compiled, copy it in the same directory as your .nc file and run 

./streamfunction.e

The script will ask you for the name of your .nc file, and will run and produce a new nameofyourfile_stream.nc file.

Be careful : In this new file, all fields are temporally and zonally averaged.

If you want to use python instead of fortran, you can take a look at this repo. It hosts a tool to perform dynamical analysis of GCM simulations (and therefore, it computes the mass stream function and a lot of other stuff), but it is tailored for Dynamico only.

Continuing Simulations

At the end of a simulation, the model generates restart files (files 'restart.nc' and 'restartfi.nc') which contain the final state of the model. The 'restart.nc' and 'restartfi.nc' files have the same format as the 'start.nc' and 'startfi.nc' files, respectively.

These files can in fact be used as initial states to continue the simulation, using the following renaming command lines: 

mv restart.nc start.nc
mv restartfi.nc startfi.nc

Running a simulation with these start files will in fact resume the simulation from where the previous run ended.

bash scripts

We have set up very simple bash scripts to automatize the launching of chain simulations. Here is an example: 

#!/bin/bash
###########################################################################
# Script to perform several chained LMD Mars GCM simulations
# SET HERE the maximum total number of simulations

nummax=200

###########################################################################


echo "---------------------------------------------------------"
echo "STARTING LOOP RUN"
echo "---------------------------------------------------------"

dir=`pwd`
machine=`hostname`
address=`whoami`

# Look for file "num_run" which should contain 
# the value of the previously computed season
# (defaults to 0 if file "num_run" does not exist)
if [[ -r num_run ]] ; then
  echo "found file num_run"
  numold=`cat num_run`
else
  numold=0
fi
echo "numold is set to" ${numold}


# Set value of current season 
(( numnew = ${numold} + 1 ))
echo "numnew is set to" ${numnew}

# Look for initialization data files (exit if none found)
if [[ ( -r start${numold}.nc  &&  -r startfi${numold}.nc ) ]] ; then
   \cp -f start${numold}.nc start.nc
   \cp -f startfi${numold}.nc startfi.nc
else
   if (( ${numold} == 99999 )) ; then
    echo "No run because previous run crashed ! (99999 in num_run)"
    exit
   else
   echo "Where is file start"${numold}".nc??"
   exit
   fi
fi

# Run GCM
mpirun -np 4 gcm_64x48x26_phystd_para.e < diagfi.def > lrun${numnew}


# Check if run ended normaly and copy datafiles
if [[ ( -r restartfi.nc  &&  -r restart.nc ) ]] ; then
  echo "Run seems to have ended normaly"


  \mv -f restart.nc start${numnew}.nc
  \mv -f restartfi.nc startfi${numnew}.nc  
    
else
  if [[ -r num_run ]] ; then
    \mv -f num_run num_run.crash
  else
    echo "No file num_run to build num_run.crash from !!"
    # Impose a default value of 0 for num_run
    echo 0 > num_run.crash
  fi
 echo 99999 > num_run
############## To receive an Email message if the run crashes ########
mail -s "crash run GCM" $address <<ENDMAIL
The run on $machine in $dir has just crashed.
ENDMAIL
############################################"" 
 exit
fi

# Copy other datafiles that may have been generated
if [[ -r diagfi.nc ]] ; then
  \mv -f diagfi.nc diagfi${numnew}.nc
fi
if [[ -r diagsoil.nc ]] ; then
  \mv -f diagsoil.nc diagsoil${numnew}.nc
fi
if [[ -r stats.nc ]] ; then
  \mv -f stats.nc stats${numnew}.nc
fi
if [[ -f profiles.dat ]] ; then
  \mv -f profiles.dat profiles${numnew}.dat
  \mv -f profiles.hdr profiles${numnew}.hdr
fi

# Prepare things for upcoming runs by writing
# value of computed season in file num_run
echo ${numnew} > num_run

# If we are over nummax : stop
if (( $numnew + 1 > $nummax )) ; then
   exit
else
   \cp -f run_gnome exe_mars
   ./exe_mars
fi

Visualization software

Panoply

Screenshot of panoply showing here LMD Generic results for the exoplanet TRAPPIST-1e

ncview

paraview

planetoplot

python scripts

TO BE COMPLETED

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