run_nemo.md

@@ -19,9 +19,9 @@
 _Working environment_:
 
    a)  WORKDIR (prepare jobs, inputs):
-    ```console
-    $WRKDIR/NEMO_CFGS/models/NEMO/dev_XXXXX_config_legos/cfgs/$CONFIG_CASE/
    
+    ```console
+    on $WRKDIR/NEMO_CFGS/models/NEMO/dev_XXXXX_config_legos/cfgs/$CONFIG_CASE/:
     *   BLD/      ===> Built and preprocessed libraries"
     *   EXP00/    ===> Rundir"
     *   MY_SRC/   ===> Fortran user routines"
@@ -30,16 +30,20 @@ _Working environment_:
     ```
     
    Inputs are here:
+   
     ```console
     $WRKDIR/NEMO_CFGS/input/CONFIG
     ```
     Links are made from these files to the run directory (see below)
    
    b) SCRATCH (run directory)
+   
     ```console  
     $SCRATCHDIR/TMP/${CONFIG_CASE}_X/*  (X car on peut faire des jobs en cascade.. un run par an par exemple..., le run suivant auquel cas sera initialisé avec le restart précédemment crée, A noter que cette le nombre de jobs à exécuter est spécifié dans includefiles.ksh MAXSUB)
     ```
+    
    c) STORE (the results (diagnostics, outputs and restart))
+   
     ```console
     $SDIR/$CONFIG_CASE-(S|R)/*
     ```
@@ -53,12 +57,11 @@ _rundir_:
 Normally now, you have something like this on your directory: 
 
 ```
-NEMO_CFGS/models/NEMO/dev_XXXXX_config_legos/cfgs/CONFIG_CASE/EXP00/
-
+on NEMO_CFGS/models/NEMO/dev_XXXXX_config_legos/cfgs/CONFIG_CASE/EXP00/ : 
 
-namelist_top_ref -> ../../SHARED/namelist_top_ref
-namelist_ref -> ../../SHARED/namelist_ref
-namelist_pisces_ref -> ../../SHARED/namelist_pisces_ref
+namelist_top_ref
+namelist_ref
+namelist_pisces_ref
 iodef.xml
 nemo.exe -> nemo
 namelist_pisces_cfg