Review comments and no-1d chunking

cicecore/cicedyn/analysis/ice_history_shared.F90

@@ -62,11 +62,9 @@ module ice_history_shared
       integer (kind=int_kind), public :: &
          history_iotasks     , & ! iotasks, root, stride defines io pes for pio
          history_root        , & ! iotasks, root, stride defines io pes for pio
-         history_stride          ! iotasks, root, stride defines io pes for pio
-
-      integer (kind=int_kind), public :: history_deflate ! compression level for netcdf4
-
-      integer (kind=int_kind), dimension(2), public :: history_chunksize ! chunksize for netcdf4
+         history_stride      , & ! iotasks, root, stride defines io pes for pio
+         history_deflate     , & ! compression level for hdf5/netcdf4
+         history_chunksize(2) ! chunksize for hdf5/netcdf4
 
       !---------------------------------------------------------------
       ! Instructions for adding a field: (search for 'example')

cicecore/cicedyn/general/ice_init.F90

@@ -350,7 +350,7 @@ subroutine input_data
       history_file = 'iceh'  ! history file name prefix
       history_precision = 4  ! precision of history files
       history_deflate = 0    ! compression level for netcdf4
-      history_chunksize = (/0,0/) ! chunksize for netcdf4
+      history_chunksize(:) = 0 ! chunksize for netcdf4
       write_ic = .false.     ! write out initial condition
       cpl_bgc = .false.      ! couple bgc thru driver
       incond_dir = history_dir ! write to history dir for default
@@ -372,7 +372,7 @@ subroutine input_data
       restart_iotasks = -99  ! restart iotasks, root, stride sets pes for pio
       restart_rearranger = 'default'  ! restart rearranger for pio
       restart_deflate = 0    ! compression level for netcdf4
-      restart_chunksize = (/0,0/) ! chunksize for netcdf4
+      restart_chunksize(:) = 0    ! chunksize for netcdf4
       lcdf64       = .false.      ! 64 bit offset for netCDF
       ice_ic       = 'default'    ! latitude and sst-dependent
       grid_format  = 'bin'        ! file format ('bin'=binary or 'nc'=netcdf)
@@ -953,8 +953,7 @@ subroutine input_data
       call broadcast_scalar(history_rearranger,   master_task)
       call broadcast_scalar(hist_time_axis,       master_task)
       call broadcast_scalar(history_deflate,      master_task)
-      call broadcast_scalar(history_chunksize(1), master_task)
-      call broadcast_scalar(history_chunksize(2), master_task)
+      call broadcast_array(history_chunksize,     master_task)
       call broadcast_scalar(write_ic,             master_task)
       call broadcast_scalar(cpl_bgc,              master_task)
       call broadcast_scalar(incond_dir,           master_task)
@@ -972,8 +971,7 @@ subroutine input_data
       call broadcast_scalar(restart_stride,       master_task)
       call broadcast_scalar(restart_rearranger,   master_task)
       call broadcast_scalar(restart_deflate,      master_task)
-      call broadcast_scalar(restart_chunksize(1), master_task)
-      call broadcast_scalar(restart_chunksize(2), master_task)
+      call broadcast_array(restart_chunksize,     master_task)
       call broadcast_scalar(lcdf64,               master_task)
       call broadcast_scalar(pointer_file,         master_task)
       call broadcast_scalar(ice_ic,               master_task)
@@ -1769,34 +1767,17 @@ subroutine input_data
       if (history_deflate/=0 .or. restart_deflate/=0 &
          .or. history_chunksize(1)/=0 .or. history_chunksize(2)/=0 &
          .or. restart_chunksize(1)/=0 .or. restart_chunksize(2)/=0) then
-         if (my_task == master_task) then
-            write (nu_diag,*) subname//' WARNING: _deflate and _chunksize not compatible with PIO1, will be ignored'
-         endif
-#else
-      if(history_deflate<0 .or. history_deflate>9) then
-         if (my_task == master_task) then
-            write (nu_diag,*) subname//' WARNING: history_deflate value not valid, setting to 0 '
-            write (nu_diag,*) subname//' WARNING: Allowed range: integers from 0 to 9 '
-         endif
-         history_deflate=0
-      endif
-
-      if(restart_deflate<0 .or. restart_deflate>9) then
-         if (my_task == master_task) then
-            write (nu_diag,*) subname//' WARNING: restart_deflate value not valid, setting to 0 '
-            write (nu_diag,*) subname//' WARNING: Allowed range: integers from 0 to 9 '
-         endif
-         restart_deflate=0
+         if (my_task == master_task) write (nu_diag,*) subname//' ERROR: _deflate and _chunksize not compatible with PIO1'
+         abort_list = trim(abort_list)//":54"
       endif
-
+#else 
 #ifndef CESMCOUPLED
       ! history_format not used by nuopc driver
       if (history_format/='hdf5' .and. history_deflate/=0) then
          if (my_task == master_task) then
             write (nu_diag,*) subname//' WARNING: history_deflate not compatible with '//history_format
             write (nu_diag,*) subname//' WARNING: netcdf compression only possible with history_type="hdf5" '
          endif
-         history_deflate=0
       endif
 
       if (history_format/='hdf5' .and. (history_chunksize(1)/=0 .or. history_chunksize(2)/=0)) then
@@ -1811,7 +1792,6 @@ subroutine input_data
             write (nu_diag,*) subname//' WARNING: restart_deflate not compatible with '//restart_format
             write (nu_diag,*) subname//' WARNING: netcdf compression only possible with restart_type="hdf5" '
          endif
-         restart_deflate=0
       endif
 
       if (restart_format/='hdf5' .and. (restart_chunksize(1)/=0 .or. restart_chunksize(2)/=0)) then
@@ -1820,8 +1800,19 @@ subroutine input_data
             write (nu_diag,*) subname//' WARNING: netcdf chunking only possible with restart_type="hdf5" '
          endif
       endif
-
 #endif
+
+   if(history_deflate<0 .or. history_deflate>9) then
+      if (my_task == master_task) write (nu_diag,*) subname//&
+         ' ERROR: history_deflate value not valid. Allowed range: integers from 0 to 9 '
+      abort_list = trim(abort_list)//":55"
+   endif
+
+   if(restart_deflate<0 .or. restart_deflate>9) then
+      if (my_task == master_task) write (nu_diag,*) subname//&
+         ' ERROR: restart_deflate value not valid. Allowed range: integers from 0 to 9 '
+      abort_list = trim(abort_list)//":56"
+   endif
 #endif
 
       ! Implicit solver input validation

cicecore/cicedyn/infrastructure/io/io_netcdf/ice_history_write.F90

@@ -45,6 +45,8 @@ module ice_history_write
 
       public :: ice_write_hist
 
+      integer (kind=int_kind) :: imtid,jmtid
+
 !=======================================================================
 
       contains
@@ -90,7 +92,7 @@ subroutine ice_write_hist (ns)
       real (kind=dbl_kind), dimension(nx_block,ny_block,max_blocks) :: work1
 
       integer (kind=int_kind) :: i,k,ic,n,nn, &
-         ncid,status,imtid,jmtid,kmtidi,kmtids,kmtidb, cmtid,timid,varid, &
+         ncid,status,kmtidi,kmtids,kmtidb, cmtid,timid,varid, &
          nvertexid,ivertex,kmtida,iflag, fmtid
       integer (kind=int_kind), dimension(3) :: dimid
       integer (kind=int_kind), dimension(4) :: dimidz
@@ -454,9 +456,9 @@ subroutine ice_write_hist (ns)
             endif
          enddo
 
-      !-----------------------------------------------------------------
-      ! define attributes for time-variant variables
-      !-----------------------------------------------------------------
+         !-----------------------------------------------------------------
+         ! define attributes for time-variant variables
+         !-----------------------------------------------------------------
 
          do n=1,num_avail_hist_fields_2D
             if (avail_hist_fields(n)%vhistfreq == histfreq(ns) .or. write_ic) then
@@ -475,31 +477,43 @@ subroutine ice_write_hist (ns)
             endif
          enddo  ! num_avail_hist_fields_3Dc
 
+         dimidz(1) = imtid
+         dimidz(2) = jmtid
          dimidz(3) = kmtidi
+         dimidz(4) = timid
 
          do n = n3Dccum + 1, n3Dzcum
             if (avail_hist_fields(n)%vhistfreq == histfreq(ns) .or. write_ic) then
                call ice_hist_field_def(ncid, avail_hist_fields(n),lprecision, dimidz,ns)
             endif
          enddo  ! num_avail_hist_fields_3Dz
 
+         dimidz(1) = imtid
+         dimidz(2) = jmtid
          dimidz(3) = kmtidb
+         dimidz(4) = timid
 
          do n = n3Dzcum + 1, n3Dbcum
             if (avail_hist_fields(n)%vhistfreq == histfreq(ns) .or. write_ic) then
                call ice_hist_field_def(ncid, avail_hist_fields(n),lprecision, dimidz,ns)
             endif
          enddo  ! num_avail_hist_fields_3Db
 
+         dimidz(1) = imtid
+         dimidz(2) = jmtid
          dimidz(3) = kmtida
+         dimidz(4) = timid
 
          do n = n3Dbcum + 1, n3Dacum
             if (avail_hist_fields(n)%vhistfreq == histfreq(ns) .or. write_ic) then
                call ice_hist_field_def(ncid, avail_hist_fields(n),lprecision, dimidz,ns)
             endif
          enddo  ! num_avail_hist_fields_3Da
 
+         dimidz(1) = imtid
+         dimidz(2) = jmtid
          dimidz(3) = fmtid
+         dimidz(4) = timid
 
          do n = n3Dacum + 1, n3Dfcum
             if (avail_hist_fields(n)%vhistfreq == histfreq(ns) .or. write_ic) then
@@ -519,15 +533,23 @@ subroutine ice_write_hist (ns)
             endif
          enddo  ! num_avail_hist_fields_4Di
 
+         dimidcz(1) = imtid
+         dimidcz(2) = jmtid
          dimidcz(3) = kmtids
+         dimidcz(4) = cmtid
+         dimidcz(5) = timid
 
          do n = n4Dicum + 1, n4Dscum
             if (avail_hist_fields(n)%vhistfreq == histfreq(ns) .or. write_ic) then
                call ice_hist_field_def(ncid, avail_hist_fields(n),lprecision, dimidcz,ns)
             endif
          enddo  ! num_avail_hist_fields_4Ds
 
+         dimidcz(1) = imtid
+         dimidcz(2) = jmtid
          dimidcz(3) = fmtid
+         dimidcz(4) = cmtid
+         dimidcz(5) = timid
 
          do n = n4Dscum + 1, n4Dfcum
             if (avail_hist_fields(n)%vhistfreq == histfreq(ns) .or. write_ic) then
@@ -1155,7 +1177,7 @@ subroutine ice_hist_field_def(ncid, hfield, lprecision, dimids, ns)
             history_precision, hist_avg
          use ice_calendar, only: histfreq, histfreq_n, write_ic
 #ifdef USE_NETCDF
-         use netcdf, only: NF90_CHUNKED, nf90_def_var, nf90_put_att
+         use netcdf, only: NF90_CHUNKED, nf90_def_var, nf90_put_att, nf90_def_var_chunking, nf90_def_var_deflate
 
          integer(kind=int_kind), intent(in) :: ncid, dimids(:), lprecision, ns
          type(ice_hist_field), intent(in) :: hfield
@@ -1164,24 +1186,25 @@ subroutine ice_hist_field_def(ncid, hfield, lprecision, dimids, ns)
          integer(kind=int_kind) :: chunks(size(dimids)), i, status, varid
 
          character(len=*), parameter :: subname = '(ice_hist_field_def)'
-
-         if (history_format=='hdf5') then 
-            chunks(1)=history_chunksize(1)
-            chunks(2)=history_chunksize(2)
-            do i = 3, size(dimids)
-               chunks(i) = 0
-            enddo
-            status = nf90_def_var(ncid, hfield%vname, &
-               lprecision, dimids, varid, &
-               chunksizes=chunks, deflate_level=history_deflate)
-            call ice_check_nc(status, &
-               subname//' ERROR: defining var '//hfield%vname,file=__FILE__,line=__LINE__)
-         else 
-            ! no chunk and compress
-            status = nf90_def_var(ncid, hfield%vname, &
-               lprecision, dimids, varid)
-            call ice_check_nc(status, &
-               subname//' ERROR: defining var '//hfield%vname,file=__FILE__,line=__LINE__)
+
+         status = nf90_def_var(ncid, hfield%vname, lprecision, dimids, varid)
+         call ice_check_nc(status, subname//' ERROR: defining var '//trim(hfield%vname),file=__FILE__,line=__LINE__)
+
+         if (history_format=='hdf5' .and. size(dimids)>1) then
+            if (dimids(1)==imtid .and. dimids(2)==jmtid) then
+               chunks(1)=history_chunksize(1)
+               chunks(2)=history_chunksize(2)
+               do i = 3, size(dimids)
+                  chunks(i) = 0
+               enddo
+               status = nf90_def_var_chunking(ncid,varid, NF90_CHUNKED, chunksizes=chunks)
+               call ice_check_nc(status, subname//' ERROR chunking var '//trim(hfield%vname), file=__FILE__, line=__LINE__)
+            endif
+         endif
+
+         if (history_format=='hdf5' .and. history_deflate/=0) then
+            status=nf90_def_var_deflate(ncid, varid, shuffle=0, deflate=1, deflate_level=history_deflate)
+            call ice_check_nc(status, subname//' ERROR deflating var '//trim(hfield%vname), file=__FILE__, line=__LINE__)
          endif
 
       ! add attributes
@@ -1300,32 +1323,39 @@ end subroutine ice_write_hist_fill
 
       subroutine ice_hist_coord_def(ncid, coord, lprecision, dimids, varid)
 
-         use ice_history_shared, only: history_deflate, history_format
+         use ice_history_shared, only: history_deflate, history_format, history_chunksize
 #ifdef USE_NETCDF
-         use netcdf, only: nf90_def_var, nf90_put_att
+         use netcdf, only: nf90_def_var, nf90_put_att, nf90_def_var_chunking, nf90_def_var_deflate, NF90_CHUNKED
 
          integer(kind=int_kind), intent(in) :: ncid, dimids(:), lprecision
          type(coord_attributes), intent(in) :: coord
          integer(kind=int_kind), intent(inout) :: varid
 
          !local vars
-         integer(kind=int_kind) :: status
+         integer(kind=int_kind) ::chunks(size(dimids)), i, status
 
          character(len=*), parameter :: subname = '(ice_hist_coord_def)'
+
+         status = nf90_def_var(ncid, coord%short_name, lprecision, dimids, varid)
+         call ice_check_nc(status, subname//' ERROR: defining coord '//coord%short_name,file=__FILE__,line=__LINE__)
 
-         !define var, set deflate, long_name and units
-         if (history_format=='hdf5' .and. size(dimids)>1 ) then
-            status = nf90_def_var(ncid, trim(coord%short_name), &
-               lprecision, dimids, varid, deflate_level=history_deflate)
-            call ice_check_nc(status, &
-               subname//' ERROR: defining coord '//coord%short_name,file=__FILE__,line=__LINE__)
-         else 
-            ! no compress
-            status = nf90_def_var(ncid, coord%short_name, &
-               lprecision, dimids, varid)
-            call ice_check_nc(status, &
-               subname//' ERROR: defining coord '//coord%short_name,file=__FILE__,line=__LINE__)
+         if (history_format=='hdf5' .and. size(dimids)>1) then
+            if (dimids(1)==imtid .and. dimids(2)==jmtid) then
+               chunks(1)=history_chunksize(1)
+               chunks(2)=history_chunksize(2)
+               do i = 3, size(dimids)
+                  chunks(i) = 0
+               enddo
+               status = nf90_def_var_chunking(ncid,varid, NF90_CHUNKED, chunksizes=chunks)
+               call ice_check_nc(status, subname//' ERROR chunking var '//trim(coord%short_name), file=__FILE__, line=__LINE__)
+            endif
+         endif
+
+         if (history_format=='hdf5' .and. history_deflate/=0) then
+            status=nf90_def_var_deflate(ncid, varid, shuffle=0, deflate=1, deflate_level=history_deflate)
+            call ice_check_nc(status, subname//' ERROR deflating var '//trim(coord%short_name), file=__FILE__, line=__LINE__)
          endif
+
          status = nf90_put_att(ncid,varid,'long_name',trim(coord%long_name))
          call ice_check_nc(status, subname// ' ERROR: defining long_name for '//coord%short_name, &
                            file=__FILE__, line=__LINE__)

cicecore/cicedyn/infrastructure/io/io_netcdf/ice_restart.F90

@@ -30,10 +30,12 @@ module ice_restart
       implicit none
       private
       public :: init_restart_write, init_restart_read, &
-                read_restart_field, write_restart_field, final_restart, &
-                query_field
+         read_restart_field, write_restart_field, final_restart, &
+         query_field
 
-      integer (kind=int_kind) :: ncid
+      integer (kind=int_kind) :: ncid , &
+         dimid_ni,   & ! netCDF identifiers
+         dimid_nj
 
 !=======================================================================
 
@@ -170,8 +172,7 @@ subroutine init_restart_write(filename_spec)
       integer (kind=int_kind), allocatable :: dims(:)
 
       integer (kind=int_kind) :: &
-        dimid_ni,   & ! netCDF identifiers
-        dimid_nj,   & !
+
         dimid_ncat, & !
         iflag,      & ! netCDF creation flag
         status        ! status variable from netCDF routine
@@ -890,18 +891,26 @@ subroutine define_rest_field(ncid, vname, dims)
 
 #ifdef USE_NETCDF
 
-      if (restart_format=='hdf5') then
-         chunks(1)=restart_chunksize(1)
-         chunks(2)=restart_chunksize(2)
-         do i = 3, size(dims)
-            chunks(i) = 0
-         enddo
-         status = nf90_def_var(ncid,trim(vname),nf90_double,dims,varid, &
-            chunksizes=chunks, deflate_level=restart_deflate)
-      else
-         status = nf90_def_var(ncid,trim(vname),nf90_double,dims,varid)
-      end if
+      status = nf90_def_var(ncid,trim(vname),nf90_double,dims,varid)
       call ice_check_nc(status, subname//' ERROR: def var '//trim(vname), file=__FILE__, line=__LINE__)
+
+      if (restart_format=='hdf5' .and. size(dims)>1) then
+         if (dims(1)==dimid_ni .and. dims(2)==dimid_nj) then
+            chunks(1)=restart_chunksize(1)
+            chunks(2)=restart_chunksize(2)
+            do i = 3, size(dims)
+               chunks(i) = 0
+            enddo
+            status = nf90_def_var_chunking(ncid,varid, NF90_CHUNKED, chunksizes=chunks)
+            call ice_check_nc(status, subname//' ERROR: chunking var '//trim(vname), file=__FILE__, line=__LINE__)
+         endif
+      endif
+
+      if (restart_format=='hdf5' .and. restart_deflate/=0) then
+         status=nf90_def_var_deflate(ncid, varid, shuffle=0, deflate=1, deflate_level=restart_deflate)
+         call ice_check_nc(status, subname//' ERROR deflating var '//trim(vname), file=__FILE__, line=__LINE__)
+      endif
+
 #else
       call abort_ice(subname//' ERROR: USE_NETCDF cpp not defined', &
           file=__FILE__, line=__LINE__)