.. _ doc.environment:

MARS environnement : Summary 
=============================

 * **create one config, compilation, correction of subroutine ..**
          * *mkconfdir CONF CASE (rank)*
          *  edit makefile and choose test case if you are using a testcase
          * *gmake install*
          *  edit makefile and choose the RANK
          * *gmake*
          * *getfile WORK/casvortex.F90* to correct a subroutine for example casvortex.F90 : 

 * **files in $UDIR/CONF/CONF-CASE :**
          * makefile
          * Makefile.datarmor[_rankX]
          * tree of the reference code INC; PHYS/'*'; BIOLO; TRAJ; SEDIM; SWAN; ..
          * WORK/all the routines of the reference code (link to $CDIR)
          * Version (contains used $HOMEMARS)
          * smallf90[_rankX] (link to $CDIR)
          * subroutines you want to correct (type getfile WORK/subroutine.F90 before)
              . example : PHYS/KTEST/casvortex.F90
              . example : casvortex.F90 (link to PHYS/KTEST/casvortex.F90)

 * **compile MARS after change of user subroutines**
          * edit and modify *casvortex.F90* 
          * edit makefile and choose the RANK 
          * edit Makefile.datarmor[_rankX] and choose CPP keys and compiling options
          * then compile (*gmake*)

 * **files in $CDIR/WCONF-CASE**
          * copy of the entire reference code
          * WORK contains all the routine (links to PHYS/'*'…)
          * smallf90[_rankX] contains all the compiled routines after preprocessing

 * **files in $RDIR/CONF/CONF-CASE**
          * namelists : paramain.txt, paraspec.txt, paracom.txt, parasubs.txt,parasedim.txt,parabiolo.txt, paraconta.tt, parawave.txt..
          * output.dat
          * batch_seq, batch_omp, runmpi_connect (which uses batch_mpi and batch_connect(bydate) ), runmpt_connect…
          * mpi.txt (for MPI purpose)
          * mars_exe

 * **Before running, the user has to :**
          * define all the parameters in the different namelist (para*)
          * under inputs directory, define head.CONF
          * under inputs directory, add the input files (like bathymetry, initial condition, open boundary conditions…)
          * under inputs directory, define all default .dat files read by the simulation (ex river.dat, outflox.dat, variable.dat...)