Add ability to write out one-time grid history file (CICE-Consortium#1005)

Add ability to write one-time grid file in netCDf and PIO history features
- Add grid_outfile logical namelist
- Add extra history stream to be used just for grid output file, that stream is designated with the histfreq='g' label. It's turned on with the logical grid_outfile namelist and then automatically turned off after it's written the first time. This happens in ice_history.F90.
- Add logic in ice_history_write.F90 to explicitly write the grid fields to the grid history file.
- The one time grid filename is iceh_grid.nc
- Add grid_outfile=.true. to set_nml.histall
- Add external_variables global attribute to history files to note grid fields that are expected to be on other files
- Add date_created global attribute

Fix bug in PIO where 5d variables had their two "z" axis coordinates reversed when writing the field even though the variable had the correct axes defined in the history file. Detected by comparing netCDF and PIO history files.

Set history netcdf attribute Conventions to CF-1.8. Ran history files through a CF checker. This resulted in a couple of warning messages but no errors. If grid variables associated with variable coordinate attributes are removed from the history file, this will result in CF errors even though external_variables are defined. This is sort of a shortcoming in the current CF conventions, but we decided to move ahead anyway. CF compliance will only be broken if grid variables are turned off in history files, and they are defined as part of other variable's coordinate (or similar) attributes.

Add axis to the history coord_attributes datatype to provide another attribute on the netcdf file. Set axis to 'X', 'Y', or 'T' to a small subset of history file coordinate variables.

Change netcdf "unitless" unit to "1".

Update some abort calls in ice_history.F90

Update version_name namelist implementation, was not being broadcast or written to the log file. Affected history file output.

Remove hist namelist settings in set_nml.run* files to minimize conflicts with other namelist options groups.

Add a test case that allows manual comparison of netCDF and PIO history files. This needs to be done with cprnc. cmp of restart files and diff of log files produce differences even when results are bit-for-bit identical.

Update documentation

Author: apcraig

cicecore/cicedyn/analysis/ice_history.F90

@@ -69,7 +69,7 @@ subroutine init_hist (dt)
       use ice_domain_size, only: max_blocks, max_nstrm, nilyr, nslyr, nblyr, ncat, nfsd
       use ice_dyn_shared, only: kdyn
       use ice_flux, only: mlt_onset, frz_onset, albcnt, snwcnt
-      use ice_grid, only: grid_ice, &
+      use ice_grid, only: grid_ice, grid_outfile, &
           grid_atm_thrm, grid_atm_dynu, grid_atm_dynv, &
           grid_ocn_thrm, grid_ocn_dynu, grid_ocn_dynv
       use ice_history_shared ! everything
@@ -239,15 +239,14 @@ subroutine init_hist (dt)
          call get_fileunit(nu_nml)
          open (nu_nml, file=trim(nml_filename), status='old',iostat=nml_error)
          if (nml_error /= 0) then
-            call abort_ice(subname//'ERROR: '//trim(nml_name)//' open file '// &
-               trim(nml_filename), &
-               file=__FILE__, line=__LINE__)
+            call abort_ice(subname//' ERROR: '//trim(nml_name)//' open file '// &
+               trim(nml_filename), file=__FILE__, line=__LINE__)
          endif
 
          ! seek to this namelist
          call goto_nml(nu_nml,trim(nml_name),nml_error)
          if (nml_error /= 0) then
-            call abort_ice(subname//'ERROR: searching for '// trim(nml_name), &
+            call abort_ice(subname//' ERROR: searching for '// trim(nml_name), &
                file=__FILE__, line=__LINE__)
          endif
 
@@ -260,7 +259,7 @@ subroutine init_hist (dt)
                ! backspace and re-read erroneous line
                backspace(nu_nml)
                read(nu_nml,fmt='(A)') tmpstr2
-               call abort_ice(subname//'ERROR: ' // trim(nml_name) // ' reading ' // &
+               call abort_ice(subname//' ERROR: ' // trim(nml_name) // ' reading ' // &
                     trim(tmpstr2), file=__FILE__, line=__LINE__)
             endif
          end do
@@ -278,23 +277,35 @@ subroutine init_hist (dt)
                 nstreams = nstreams + 1
                 if (ns >= 2) then
                    if (histfreq(ns-1) == 'x') then
-                      call abort_ice(subname//'ERROR: histfreq all non x must be at start of array')
+                      call abort_ice(subname//' ERROR: histfreq all non x must be at start of array', &
+                           file=__FILE__, line=__LINE__)
                    endif
                 endif
          else if (histfreq(ns) /= 'x') then
-             call abort_ice(subname//'ERROR: histfreq contains illegal element')
+             write(nu_diag, * ) subname,' ns,histfreq = ',ns,histfreq(ns)
+             call abort_ice(subname//' ERROR: histfreq contains illegal element', &
+                  file=__FILE__, line=__LINE__)
          endif
       enddo
-      if (nstreams == 0) write (nu_diag,*) 'WARNING: No history output'
+      if (nstreams == 0 .and. my_task == master_task) write (nu_diag,*) subname,' WARNING: No history output'
       do ns1 = 1, nstreams
          do ns2 = 1, nstreams
             if (histfreq(ns1) == histfreq(ns2) .and. ns1/=ns2 &
                .and. my_task == master_task) then
-               call abort_ice(subname//'ERROR: histfreq elements must be unique')
+               call abort_ice(subname//' ERROR: histfreq elements must be unique', &
+                    file=__FILE__, line=__LINE__)
             endif
          enddo
       enddo
 
+      ! Turn on one-time grid output file
+      if (grid_outfile) then
+         nstreams = nstreams + 1
+         histfreq(nstreams) = 'g'
+         hist_avg(nstreams) = .false.
+         if (my_task == master_task) write (nu_diag,*) subname,' Writing one-time grid file'
+      endif
+
       if (.not. tr_iage) then
          f_iage = 'x'
          f_dagedtt = 'x'
@@ -445,14 +456,6 @@ subroutine init_hist (dt)
          f_taubyE = f_tauby
       endif
 
-      ! write dimensions for 3D or 4D history variables
-      ! note: list of variables checked here is incomplete
-      if (f_aicen(1:1) /= 'x' .or. f_vicen(1:1) /= 'x' .or. &
-          f_Tinz (1:1) /= 'x' .or. f_Sinz (1:1) /= 'x') f_NCAT  = .true.
-      if (f_Tinz (1:1) /= 'x' .or. f_Sinz (1:1) /= 'x') f_VGRDi = .true.
-      if (f_Tsnz (1:1) /= 'x')                          f_VGRDs = .true.
-      if (tr_fsd)                                       f_NFSD  = .true.
-
       call broadcast_scalar (f_tlon, master_task)
       call broadcast_scalar (f_tlat, master_task)
       call broadcast_scalar (f_ulon, master_task)
@@ -4195,6 +4198,13 @@ subroutine accum_hist (dt)
         enddo
 
       endif  ! write_history or write_ic
+
+      ! Turn off one-time grid output file
+      if (histfreq(ns) == 'g') then
+         histfreq(ns) = 'x'
+         nstreams = nstreams - 1
+      endif
+
       enddo  ! nstreams
 
       !$OMP PARALLEL DO PRIVATE(iblk,i,j,ilo,ihi,jlo,jhi,this_block)

cicecore/cicedyn/analysis/ice_history_shared.F90

@@ -822,12 +822,22 @@ subroutine construct_filename(ncfile,suffix,ns)
                  write(ncfile,'(a,a,i4.4,a,a)') &
                        history_file(1:lenstr(history_file))//trim(cstream),'.', &
                        iyear,'.',trim(suffix)
+              elseif (histfreq(ns) == 'g') then
+                 write(ncfile,'(a,a,a,a)')  &
+                       history_file(1:lenstr(history_file)),'_grid', &
+                       '.',trim(suffix)
               endif
 
            else                     ! instantaneous
-              write(ncfile,'(a,a,i4.4,a,i2.2,a,i2.2,a,i5.5,a,a)')  &
-                    history_file(1:lenstr(history_file))//trim(cstream),'_inst.', &
-                    iyear,'-',imonth,'-',iday,'-',msec,'.',trim(suffix)
+              if (histfreq(ns) == 'g') then
+                 write(ncfile,'(a,a,a,a)')  &
+                       history_file(1:lenstr(history_file)),'_grid', &
+                       '.',trim(suffix)
+              else
+                 write(ncfile,'(a,a,i4.4,a,i2.2,a,i2.2,a,i5.5,a,a)')  &
+                       history_file(1:lenstr(history_file))//trim(cstream),'_inst.', &
+                       iyear,'-',imonth,'-',iday,'-',msec,'.',trim(suffix)
+              endif
            endif
 
         endif

cicecore/cicedyn/general/ice_init.F90

@@ -109,7 +109,7 @@ subroutine input_data
           grid_file, gridcpl_file, kmt_file, &
           bathymetry_file, use_bathymetry, &
           bathymetry_format, kmt_type, &
-          grid_type, grid_format, &
+          grid_type, grid_format, grid_outfile, &
           grid_ice, grid_ice_thrm, grid_ice_dynu, grid_ice_dynv, &
           grid_ocn, grid_ocn_thrm, grid_ocn_dynu, grid_ocn_dynv, &
           grid_atm, grid_atm_thrm, grid_atm_dynu, grid_atm_dynv, &
@@ -217,7 +217,7 @@ subroutine input_data
         ncat,           nilyr,           nslyr,         nblyr,          &
         kcatbound,      gridcpl_file,    dxrect,        dyrect,         &
         dxscale,        dyscale,         lonrefrect,    latrefrect,     &
-        scale_dxdy,                                                     &
+        scale_dxdy,     grid_outfile,                                   &
         close_boundaries, orca_halogrid, grid_ice,      kmt_type,       &
         grid_atm,       grid_ocn
 
@@ -332,6 +332,7 @@ subroutine input_data
       bfbflag = 'off'        ! off = optimized
       diag_type = 'stdout'
       diag_file = 'ice_diag.d'
+      histfreq(:) = 'x'
       histfreq(1) = '1'      ! output frequency option for different streams
       histfreq(2) = 'h'      ! output frequency option for different streams
       histfreq(3) = 'd'      ! output frequency option for different streams
@@ -383,6 +384,7 @@ subroutine input_data
       grid_atm     = 'A'          ! underlying atm forcing/coupling grid
       grid_ocn     = 'A'          ! underlying atm forcing/coupling grid
       gridcpl_file = 'unknown_gridcpl_file'
+      grid_outfile = .false.      ! write out one-time grid history file
       orca_halogrid = .false.     ! orca haloed grid - deprecated
       bathymetry_file   = 'unknown_bathymetry_file'
       bathymetry_format = 'default'
@@ -960,6 +962,7 @@ subroutine input_data
       call broadcast_scalar(cpl_bgc,              master_task)
       call broadcast_scalar(incond_dir,           master_task)
       call broadcast_scalar(incond_file,          master_task)
+      call broadcast_scalar(version_name,         master_task)
       call broadcast_scalar(dump_last,            master_task)
       call broadcast_scalar(restart_file,         master_task)
       call broadcast_scalar(restart,              master_task)
@@ -992,6 +995,7 @@ subroutine input_data
       call broadcast_scalar(grid_atm,             master_task)
       call broadcast_scalar(grid_file,            master_task)
       call broadcast_scalar(gridcpl_file,         master_task)
+      call broadcast_scalar(grid_outfile,         master_task)
       call broadcast_scalar(orca_halogrid,        master_task)
       call broadcast_scalar(bathymetry_file,      master_task)
       call broadcast_scalar(bathymetry_format,    master_task)
@@ -2529,6 +2533,7 @@ subroutine input_data
          write(nu_diag,*) '===================================== '
          if (trim(runid) /= 'unknown') &
          write(nu_diag,1031) ' runid            = ', trim(runid)
+         write(nu_diag,1031) ' version_name     = ', trim(version_name)
          write(nu_diag,1031) ' runtype          = ', trim(runtype)
          write(nu_diag,1021) ' year_init        = ', year_init
          write(nu_diag,1021) ' month_init       = ', month_init
@@ -2551,11 +2556,12 @@ subroutine input_data
          write(nu_diag,1031) ' bfbflag          = ', trim(bfbflag)
          write(nu_diag,1021) ' numin            = ', numin
          write(nu_diag,1021) ' numax            = ', numax
-         write(nu_diag,1033) ' histfreq         = ', histfreq(:)
-         write(nu_diag,1023) ' histfreq_n       = ', histfreq_n(:)
-         write(nu_diag,1033) ' histfreq_base    = ', histfreq_base(:)
-         write(nu_diag,1013) ' hist_avg         = ', hist_avg(:)
-         write(nu_diag,1033) ' hist_suffix      = ', hist_suffix(:)
+         write(nu_diag,1011) ' grid_outfile     = ', grid_outfile
+         write(nu_diag,1033) ' histfreq         = ', histfreq(1:max_nstrm-1)
+         write(nu_diag,1023) ' histfreq_n       = ', histfreq_n(1:max_nstrm-1)
+         write(nu_diag,1033) ' histfreq_base    = ', histfreq_base(1:max_nstrm-1)
+         write(nu_diag,1013) ' hist_avg         = ', hist_avg(1:max_nstrm-1)
+         write(nu_diag,1033) ' hist_suffix      = ', hist_suffix(1:max_nstrm-1)
          write(nu_diag,1031) ' history_dir      = ', trim(history_dir)
          write(nu_diag,1031) ' history_file     = ', trim(history_file)
          write(nu_diag,1021) ' history_precision= ', history_precision
@@ -2571,9 +2577,9 @@ subroutine input_data
             write(nu_diag,1039) ' Initial condition will be written in ', &
                                trim(incond_dir)
          endif
-         write(nu_diag,1033) ' dumpfreq         = ', dumpfreq(:)
-         write(nu_diag,1023) ' dumpfreq_n       = ', dumpfreq_n(:)
-         write(nu_diag,1033) ' dumpfreq_base    = ', dumpfreq_base(:)
+         write(nu_diag,1033) ' dumpfreq         = ', dumpfreq(1:max_nstrm-1)
+         write(nu_diag,1023) ' dumpfreq_n       = ', dumpfreq_n(1:max_nstrm-1)
+         write(nu_diag,1033) ' dumpfreq_base    = ', dumpfreq_base(1:max_nstrm-1)
          write(nu_diag,1011) ' dump_last        = ', dump_last
          write(nu_diag,1011) ' restart          = ', restart
          write(nu_diag,1031) ' restart_dir      = ', trim(restart_dir)

cicecore/cicedyn/infrastructure/ice_grid.F90

@@ -150,6 +150,7 @@ module ice_grid
          kmt        ! ocean topography mask for bathymetry (T-cell)
 
       logical (kind=log_kind), public :: &
+         grid_outfile,   & ! flag to write out one-time grid history file
          use_bathymetry, & ! flag for reading in bathymetry_file
          save_ghte_ghtn, & ! flag for saving global hte and htn during initialization
          scale_dxdy        ! flag to apply scale factor to vary dx/dy in rectgrid