run_nemo.md

@@ -99,25 +99,11 @@ empty
 
 ###### Prerequisites Build mesh mask
 
-User needs the mesh mask file for preprocessing on inputs, containing all geographical and grid data from the configuration. So he needs to launch the model during almost one time step, and then stop the job. The model will produce the mesh mask file. As it produce it for each mpi domains, user needs to use the rebuild_nemo tools to create it for the whole domain.   
+User needs the mesh mask file for preprocessing inputs. It contains all geographical and grid data from the configuration nemo. You need to launch the model during almost one time step, and then stop the job. The model will produce the mesh mask file. As it produce it for each mpi domains, user needs to use the rebuild_nemo tools to create it for the whole domain.   
 
-on NEMO_CONFIGS/models/NEMO/dev_XXXXX_config_legos/cfgs/CONFIG_CASE/EXP00/:
-
-1. Modify your namelist_cfg, first look on includefileini the JPNI and JPNJ variable for non-optimization use, you need to turn off the optimized MPI tiles parameters, put on section &nammpp :
-   
-   ```  
-   jpni        =   6   ! $JPNI
-   jpnj        =   23  ! $JPNJ
-   ```
-   
-   and on &namdom section
-   ```
-   ln_meshmask = .true.
-   ```
+__prerequisites__
 
-2. Modify your namelist_cfg (specific analytical without forcing input):
-
-   go to the cpp file and remove key_top key 
+   Check if specific cpp key are disabled , go to the cpp file and remove key_top key 
 
 *   bld::tool::fppkeys  ~~key_top~~ key_iomput key_mpp_mpi  key_nosignedzero
 
@@ -130,16 +116,38 @@ on NEMO_CONFIGS/models/NEMO/dev_XXXXX_config_legos/cfgs/CONFIG_CASE/EXP00/:
 > **Note** : The first step could be useless if you rebuild nemo in this way
    ./makenemo –m X64_IRENE –r TATL025BIO-XX -n CONFIG_CASE -j8 -v3 **del_key key_top** > log_build_TATL025BIO.txt 2>&1
  
+save your namelist_cfg file with another name (it will be use later) and just modify these key on your namelist_cfg file
+
+__modification of namelist_cfg file__
 
-   Then, save your namelist_cfg file with another name (it will be use later) and just modify these key on your namelist_cfg file: 
+
+on NEMO_CONFIGS/models/NEMO/dev_XXXXX_config_legos/cfgs/CONFIG_CASE/EXP00/:
+
+
+1. Modify your namelist_cfg (specific analytical without forcing input):
+ first look on includefileini the JPNI and JPNJ variable for non-optimization use, you need to turn off the optimized MPI tiles parameters, put on section &nammpp :
+   
+   ```  
+   jpni        =   6   ! $JPNI
+   jpnj        =   23  ! $JPNJ
+   ```
+   
+   and on &namdom section
+   ```
+   ln_meshmask = .true.
+   ```
+ 
+
+   Then : 
  
    ```
    ln_rstart   = .false. # No restart 
    ln_tsd_init = .false. # No IC (T et S)
+   ln_usr      = .true.  # Analytical forcing
    ln_blk      = .false. # No Bulk forcing
    ln_traqsr   = .false. # No Light penetration in the ocean
-   ln_tradmp   = .false. 
    ln_dm2dc    = .false. # No daily mean to diurnal cycle on short wave
+   ln_tradmp   = .false. # No damping term on T & S
    ln_rnf      = .false. # No runoff
    ln_bdy      = .false. # No BC
    ```
@@ -148,10 +156,10 @@ on NEMO_CONFIGS/models/NEMO/dev_XXXXX_config_legos/cfgs/CONFIG_CASE/EXP00/:
  
    ```
    ccc_msub run_nemo.ksh 
-
+   # sbatch run_nemo.ksh
    ```
 
-4. Look on your scratch the rundir path ($NOCEAN : number of procs for nemo)
+4. Look on your scratch the rundir path ($NOCEAN : number of procs for nemo) for the 1st simulation (X=1)
       ```
       cp $TOOLS_REBUILDNEMO_DIR/rebuild_nemo*  $SCRATCHDIR/TMP/${CONFIG_CASE}_X/.
       ./rebuild_nemo mesh_mask $NOCEAN