checkpoint files are geneareted by GEOSldas (#182)

* checkpoint files are generated by GEOSldas ( not MAPL) when on cubed-sphere tile space

* create year/month directories for ldas_ObsFcstAna from within GEOSldas executable

* change system() calls to Fortran2008 standard Execute_command_line()

src/Applications/LDAS_App/ldas_setup

@@ -1180,7 +1180,9 @@ class LDASsetup:
                 valn = self.catch+ensid+'_internal_checkpoint'
                 ldasrcInp[keyn]= valn
 
-                if((self.has_ldassa_pert or self.has_geos_pert) and _perturb == 1):
+                # for lat/lon and EASE tile space, specify LANDPERT checkpoint file here (via MAPL);
+                # for cube-sphere tile space, Landpert GC will set up LANDPERT checkpoint file 
+                if('-CF' not in self.rqdExeInp['GRIDNAME'] and _perturb == 1):
                     keyn = 'LANDPERT_INTERNAL_CHECKPOINT_FILE'
                     valn = 'landpert'+ensid+'_internal_checkpoint'
                     ldasrcInp[keyn]= valn

src/Components/GEOSldas_GridComp/GEOSlandassim_GridComp/clsm_ensupd_enkf_update.F90

@@ -1416,7 +1416,7 @@ subroutine output_ObsFcstAna(date_time, work_path, exp_id, &
     integer,        dimension(numprocs)       :: N_obsl_vec, tmp_low_ind
 
     character(300)                            :: fname
-
+    integer                                   :: i
 #ifdef LDAS_MPI
 
     integer                                   :: this_species, ind_tmp, j
@@ -1559,7 +1559,10 @@ subroutine output_ObsFcstAna(date_time, work_path, exp_id, &
 
        fname = get_io_filename( work_path, exp_id, file_tag, date_time=date_time, &
             dir_name=dir_name, ens_id=-1 )
+       i = index(fname, '/', .true.) 
 
+       if( i >0) call Execute_command_line('mkdir -p '//fname(1:i))
+
        open( 10, file=fname, form='unformatted', action='write')
 
        ! write header

src/Components/GEOSldas_GridComp/GEOSlandassim_GridComp/clsm_ensupd_read_obs.F90

@@ -524,7 +524,7 @@ subroutine read_obs_ae_l2_sm(                                  &
 
     cmd = '/bin/rm -f ' // tmpfname 
 
-    call system(trim(cmd))
+    call Execute_command_line(trim(cmd))
 
     ! identify all files within current assimilation interval
     ! (list all files within hourly intervals)
@@ -554,7 +554,7 @@ subroutine read_obs_ae_l2_sm(                                  &
 
        cmd = trim(cmd) // ' >> ' // trim(tmpfname)
 
-       call system(trim(cmd))
+       call Execute_command_line(trim(cmd))
 
        call augment_date_time( 3600, date_time_tmp )
 
@@ -566,7 +566,7 @@ subroutine read_obs_ae_l2_sm(                                  &
 
     cmd = 'wc -w ' // trim(tmpfname) // ' > ' // trim(tmpfname2)
 
-    call system(trim(cmd))
+    call Execute_command_line(trim(cmd))
 
     open(10, file=tmpfname2, form='formatted', action='read')
 
@@ -1037,7 +1037,7 @@ subroutine read_obs_ae_sm_LPRM(                                 &
 
     cmd = '/bin/rm -f ' // tmpfname 
 
-    call system(trim(cmd))
+    call Execute_command_line(trim(cmd))
 
     ! identify all files within current assimilation interval
     ! (list all files within hourly intervals)
@@ -1070,7 +1070,7 @@ subroutine read_obs_ae_sm_LPRM(                                 &
 
        cmd = trim(cmd) // ' >> ' // trim(tmpfname)
 
-       call system(trim(cmd))
+       call Execute_command_line(trim(cmd))
 
        call augment_date_time( 3600, date_time_tmp )
 
@@ -1082,7 +1082,7 @@ subroutine read_obs_ae_sm_LPRM(                                 &
 
     cmd = 'wc -w ' // trim(tmpfname) // ' > ' // trim(tmpfname2)
 
-    call system(trim(cmd))
+    call Execute_command_line(trim(cmd))
 
     open(10, file=tmpfname2, form='formatted', action='read')
 
@@ -1348,7 +1348,7 @@ subroutine read_obs_sm_ASCAT(                                  &
 
     cmd = '/bin/rm -f ' // tmpfname 
 
-    call system(trim(cmd))
+    call Execute_command_line(trim(cmd))
 
     ! identify all files within current assimilation interval
     ! (list all files within hourly intervals)
@@ -1379,7 +1379,7 @@ subroutine read_obs_sm_ASCAT(                                  &
 
        cmd = trim(cmd) // ' >> ' // trim(tmpfname)
 
-       call system(trim(cmd))
+       call Execute_command_line(trim(cmd))
 
 
        call augment_date_time( 3600, date_time_tmp )
@@ -1392,7 +1392,7 @@ subroutine read_obs_sm_ASCAT(                                  &
 
     cmd = 'wc -w ' // trim(tmpfname) // ' > ' // trim(tmpfname2)
 
-    call system(trim(cmd))
+    call Execute_command_line(trim(cmd))
 
     open(10, file=tmpfname2, form='formatted', action='read')
 

src/Components/GEOSldas_GridComp/Shared/LDAS_TileCoordRoutines.F90

@@ -475,7 +475,7 @@ subroutine LDAS_read_land_tile( tile_file,catch_file, tile_grid_g, tile_coord_la
 
        i=index(catch_file,'/clsm/')
        fname = catch_file(1:i)//'topo_DYN_ave_*.data'
-       call system('ls '//trim(fname) // ' >topo_DYN_ave.file')
+       call Execute_command_line('ls '//trim(fname) // ' >topo_DYN_ave.file')
        open(10,file='topo_DYN_ave.file', action='read')
        fname= ''
        read(10,'(A)') fname