# MARS procedure (Step by Step)¶

## How to set up a new configuration¶

• The grid size is defined in parameters.F90[_rank*] with imin=0, jmin=0,imax=***,jmax=***,kmax=***,
• The rank is noted in parameters.F90[_rank*] with no=*
• And the “nrac” of the configuration (4 letters) is defined parameters.F90[_rank*] (same as configuration name usually)

## Compilation with ranks¶

Each rank is compiled by modifying makefile :

cd $UDIR/CONF/CONF-CASE vi makefile, RANK = 0 gmake clean ; gmake vi makefile, RANK = 1 gmake clean ; gmake ## Choice of parametrization¶ 1. cd$RDIR/CONF/CONF-CASE
• Choice parameters and options in namelists files (namelist files)
• paramain.txt and paracom.txt are the same whatever the rank
• paraspec.txt changes for each rank
• date_startshift (if negative, date_startshift decreases as the number of the rank increases)
• l_tide_harmcompo=.true. Only for rank 0
• l_bathy_meanlev=.true. Except for the rank 0 (because taken into account in the bathymetry file)
• open boundary management in paraspec.txt;
• Look at your domain, and specify where are the open boundaries
. l_obc_east=.true./.false. (if open/closed boundary) . l_obc_west=….
• Specify the file containing the obc fields issued from an ogcm and extract executable
. file_obc_n=’../../inputs/obc_north.nc‘ . file_obc_e=…
• Which ogcm variables do you want to read and use at open boundaries ? Specify :
. l_obc_ogcm_rssh=.false. ! Read the sea surface height . l_obc_ogcm_rs=.false. ! Read the salinity . l_obc_ogcm_rt=.false. ! Read the temperature . l_obc_ogcm_ruv=.false. ! Read the barotropic velocities . l_obc_ogcm_ruvz=.false. ! Read the 3d velocities
• To relax the salinity and temperature towards the ogcm values over a bandwidth specified by obc_width
. l_obc_ogcm_relax=.true. . obc_coef_relax=0.7e-06 (time relaxation in s-1)
• others
. dtmax=1000.d0 . l_tide_harmcompo=.true.
• What kind of physics do you want to introduce through the open boundaries ?
. l_obc_ogcm=.true. ! If nested with an ogcm . l_obc_tide=.true. ! If tide and nested with a previous rank
• Which operator do you want to use ? Choose one of the following items
. l_obc_diri=.false. ! Dirichlet . l_obc_mars ! Zero gradient of velocities
• Choice of options and parameters definig outputs files in output.dat (Set up output files : output.dat)
• Build a file mpi.txt (for MPI purpose if you want to divide the domain along X AND Y) (MPI job : domain decomposition)

1. cd $RDIR/CONF/inputs • modify head.CONF (keep the same format !!!) (head.CONF) • add the input files (like bathymetry, initial condition, open boundary conditions, meteo …) • modify all default .dat files read by the simulation before any use and add the good path in namelists (ex river.dat, trajec2d*.dat, outflow.dat, variables.dat) ## Starting the run¶ 1. cd$RDIR/CONF/CONF-CASE
• Run directly if small et rapid tests with mars_exe
• or with batch_seq, batch_omp, runmpi_connect (which uses batch_mpi and batch_connect(bydate) ),
• or runmpt_connect… depending of your choice (How to run a job)