Update history_format, restart_format, add options cdf1, cdf2, cdf5,

hdf5, pnetcdf1, pnetcdf2, pnetcdf5.  Deprecate lcdf64.  But still provide
backward compatibility with old namelist.  Update test suite and
documentation.

cicecore/cicedyn/general/ice_init.F90

@@ -78,7 +78,7 @@ subroutine input_data
           restart_fsd, restart_iso, restart_snow
       use ice_restart_shared, only: &
           restart, restart_ext, restart_coszen, restart_dir, restart_file, pointer_file, &
-          runid, runtype, use_restart_time, restart_format, lcdf64
+          runid, runtype, use_restart_time, restart_format
       use ice_history_shared, only: hist_avg, history_dir, history_file, hist_suffix, &
                              incond_dir, incond_file, version_name, &
                              history_precision, history_format, hist_time_axis
@@ -163,6 +163,7 @@ subroutine input_data
       logical (kind=log_kind) :: tr_iso, tr_aero, tr_fsd, tr_snow
       logical (kind=log_kind) :: tr_pond_lvl, tr_pond_topo
       integer (kind=int_kind) :: numin, numax  ! unit number limits
+      logical (kind=log_kind) :: lcdf64  ! deprecated, backwards compatibility
 
       integer (kind=int_kind) :: rplvl, rptopo
       real (kind=dbl_kind)    :: Cf, ksno, puny, ice_ref_salinity, Tocnfrz
@@ -326,7 +327,7 @@ subroutine input_data
       histfreq_base(:) = 'zero' ! output frequency reference date
       hist_avg(:) = .true.   ! if true, write time-averages (not snapshots)
       hist_suffix(:) = 'x'   ! appended to 'history_file' in filename when not 'x'
-      history_format = 'default' ! history file format
+      history_format = 'cdf2'! history file format
       hist_time_axis = 'end' ! History file time axis averaging interval position
 
       history_dir  = './'    ! write to executable dir for default
@@ -347,7 +348,7 @@ subroutine input_data
       restart_ext  = .false. ! if true, read/write ghost cells
       restart_coszen  = .false.   ! if true, read/write coszen
       pointer_file = 'ice.restart_file'
-      restart_format = 'default'  ! restart file format
+      restart_format = 'cdf2'     ! restart file format
       lcdf64       = .false.      ! 64 bit offset for netCDF
       ice_ic       = 'default'    ! latitude and sst-dependent
       grid_format  = 'bin'        ! file format ('bin'=binary or 'nc'=netcdf)
@@ -1232,6 +1233,111 @@ subroutine input_data
          abort_list = trim(abort_list)//":1"
       endif
 
+      if (history_format /= 'cdf1'        .and. &
+          history_format /= 'cdf2'        .and. &
+          history_format /= 'cdf5'        .and. &
+          history_format /= 'hdf5'        .and. &
+          history_format /= 'pnetcdf1'    .and. &
+          history_format /= 'pnetcdf2'    .and. &
+          history_format /= 'pnetcdf5'    .and. &
+          history_format /= 'pio_netcdf'  .and. &  ! backwards compatibility
+          history_format /= 'pio_pnetcdf' .and. &  ! backwards compatibility
+          history_format /= 'default')     then    ! backwards compatibility
+         if (my_task == master_task) then
+            write(nu_diag,*) subname//' ERROR: history_format unknown = ',trim(history_format)
+         endif
+         abort_list = trim(abort_list)//":50"
+      endif
+
+      if (restart_format /= 'cdf1'        .and. &
+          restart_format /= 'cdf2'        .and. &
+          restart_format /= 'cdf5'        .and. &
+          restart_format /= 'hdf5'        .and. &
+          restart_format /= 'pnetcdf1'    .and. &
+          restart_format /= 'pnetcdf2'    .and. &
+          restart_format /= 'pnetcdf5'    .and. &
+          restart_format /= 'pio_netcdf'  .and. &  ! backwards compatibility
+          restart_format /= 'pio_pnetcdf' .and. &  ! backwards compatibility
+          restart_format /= 'default')     then    ! backwards compatibility
+         if (my_task == master_task) then
+            write(nu_diag,*) subname//' ERROR: restart_format unknown = ',trim(restart_format)
+         endif
+         abort_list = trim(abort_list)//":51"
+      endif
+
+      ! backwards compatibility
+      if (lcdf64) then
+         if (my_task == master_task) then
+            write(nu_diag,*) subname//' WARNING: lcdf64 is deprecated, please update namelist settings'
+         endif
+
+         if (history_format == 'default' .or. history_format == 'pio_netcdf') then
+            if (my_task == master_task) then
+               write(nu_diag,*) subname//' WARNING: history_format='//trim(history_format)// &
+                                ' is deprecated, please update namelist settings'
+            endif
+            history_format = 'cdf2'
+         elseif (history_format == 'pio_pnetcdf') then
+            if (my_task == master_task) then
+               write(nu_diag,*) subname//' WARNING: history_format='//trim(history_format)// &
+                                ' is deprecated, please update namelist settings'
+            endif
+            history_format = 'pnetcdf2'
+         else
+            if (my_task == master_task) then
+               write(nu_diag,*) subname//' ERROR: lcdf64 is T and history_format not supported for '//trim(history_format)
+            endif
+            abort_list = trim(abort_list)//":52"
+         endif
+
+         if (restart_format == 'default' .or. restart_format == 'pio_netcdf') then
+            if (my_task == master_task) then
+               write(nu_diag,*) subname//' WARNING: restart_format='//trim(restart_format)// &
+                                ' is deprecated, please update namelist settings'
+            endif
+            restart_format = 'cdf2'
+         elseif (restart_format == 'pio_pnetcdf') then
+            if (my_task == master_task) then
+               write(nu_diag,*) subname//' WARNING: restart_format='//trim(restart_format)// &
+                                ' is deprecated, please update namelist settings'
+            endif
+            restart_format = 'pnetcdf2'
+         else
+            if (my_task == master_task) then
+               write(nu_diag,*) subname//' ERROR: lcdf64 is T and restart_format not supported for '//trim(restart_format)
+            endif
+            abort_list = trim(abort_list)//":53"
+         endif
+      else
+         if (history_format == 'default' .or. history_format == 'pio_netcdf') then
+            if (my_task == master_task) then
+               write(nu_diag,*) subname//' WARNING: history_format='//trim(history_format)// &
+                                ' is deprecated, please update namelist settings'
+            endif
+            history_format = 'cdf1'
+         elseif (history_format == 'pio_pnetcdf') then
+            if (my_task == master_task) then
+               write(nu_diag,*) subname//' WARNING: history_format='//trim(history_format)// &
+                                ' is deprecated, please update namelist settings'
+            endif
+            history_format = 'pnetcdf1'
+         endif
+
+         if (restart_format == 'default' .or. restart_format == 'pio_netcdf') then
+            if (my_task == master_task) then
+               write(nu_diag,*) subname//' WARNING: restart_format='//trim(restart_format)// &
+                                ' is deprecated, please update namelist settings'
+            endif
+            restart_format = 'cdf1'
+         elseif (restart_format == 'pio_pnetcdf') then
+            if (my_task == master_task) then
+               write(nu_diag,*) subname//' WARNING: restart_format='//trim(restart_format)// &
+                                ' is deprecated, please update namelist settings'
+            endif
+            restart_format = 'pnetcdf1'
+         endif
+      endif
+
       if (ktransport <= 0) then
          advection = 'none'
       endif
@@ -1504,7 +1610,7 @@ subroutine input_data
             write (nu_diag,*) subname//' ERROR: snow grain radius is activated'
             write (nu_diag,*) subname//' ERROR:   Must use shortwave=dEdd or dEdd_snicar_ad'
          endif
-         abort_list = trim(abort_list)//":29"
+         abort_list = trim(abort_list)//":17"
       endif
 
       if ((rfracmin < -puny .or. rfracmin > c1+puny) .or. &
@@ -2377,7 +2483,7 @@ subroutine input_data
          write(nu_diag,1011) ' restart_ext      = ', restart_ext
          write(nu_diag,1011) ' restart_coszen   = ', restart_coszen
          write(nu_diag,1031) ' restart_format   = ', trim(restart_format)
-         write(nu_diag,1011) ' lcdf64           = ', lcdf64
+!         write(nu_diag,1011) ' lcdf64           = ', lcdf64   ! deprecated
          write(nu_diag,1031) ' restart_file     = ', trim(restart_file)
          write(nu_diag,1031) ' pointer_file     = ', trim(pointer_file)
          write(nu_diag,1011) ' use_restart_time = ', use_restart_time

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

@@ -61,7 +61,6 @@ subroutine ice_write_hist (ns)
           lont_bounds, latt_bounds, lonu_bounds, latu_bounds, &
           lonn_bounds, latn_bounds, lone_bounds, late_bounds
       use ice_history_shared
-      use ice_restart_shared, only: lcdf64
 #ifdef CESMCOUPLED
       use ice_restart_shared, only: runid
 #endif
@@ -148,8 +147,18 @@ subroutine ice_write_hist (ns)
          endif
 
          ! create file
-         iflag = nf90_clobber
-         if (lcdf64) iflag = ior(iflag,nf90_64bit_offset)
+         if (history_format == 'cdf1') then
+           iflag = nf90_clobber
+         elseif (history_format == 'cdf2') then
+           iflag = ior(nf90_clobber,nf90_64bit_offset)
+         elseif (history_format == 'cdf5') then
+           iflag = ior(nf90_clobber,nf90_64bit_data)
+         elseif (history_format == 'hdf5') then
+           iflag = ior(nf90_clobber,nf90_netcdf4)
+         else
+           call abort_ice(subname//' ERROR: history_format not allowed for '//trim(history_format), &
+              file=__FILE__, line=__LINE__)
+         endif
          status = nf90_create(ncfile(ns), iflag, ncid)
          call ice_check_nc(status, subname// ' ERROR: creating history ncfile '//ncfile(ns), &
                            file=__FILE__, line=__LINE__)

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

@@ -18,7 +18,7 @@ module ice_restart
       use ice_read_write, only: ice_check_nc
       use ice_restart_shared, only: &
           restart_ext, restart_dir, restart_file, pointer_file, &
-          runid, use_restart_time, lcdf64, lenstr, restart_coszen
+          runid, use_restart_time, lenstr, restart_coszen, restart_format
       use ice_fileunits, only: nu_diag, nu_rst_pointer
       use ice_exit, only: abort_ice
       use icepack_intfc, only: icepack_query_parameters
@@ -216,8 +216,18 @@ subroutine init_restart_write(filename_spec)
          write(nu_rst_pointer,'(a)') filename
          close(nu_rst_pointer)
 
-         iflag = 0
-         if (lcdf64) iflag = nf90_64bit_offset
+         if (restart_format == 'cdf1') then
+           iflag = nf90_clobber
+         elseif (restart_format == 'cdf2') then
+           iflag = ior(nf90_clobber,nf90_64bit_offset)
+         elseif (restart_format == 'cdf5') then
+           iflag = ior(nf90_clobber,nf90_64bit_data)
+         elseif (restart_format == 'hdf5') then
+           iflag = ior(nf90_clobber,nf90_netcdf4)
+         else
+           call abort_ice(subname//' ERROR: restart_format not allowed for '//trim(restart_format), &
+              file=__FILE__, line=__LINE__)
+         endif
          status = nf90_create(trim(filename), iflag, ncid)
          call ice_check_nc(status, subname//' ERROR: creating '//trim(filename), file=__FILE__, line=__LINE__)
 

cicecore/cicedyn/infrastructure/io/io_pio2/ice_history_write.F90

@@ -57,7 +57,7 @@ subroutine ice_write_hist (ns)
           lonn_bounds, latn_bounds, lone_bounds, late_bounds
       use ice_history_shared
       use ice_arrays_column, only: hin_max, floe_rad_c
-      use ice_restart_shared, only: runid, lcdf64
+      use ice_restart_shared, only: runid
       use ice_pio
       use pio
 
@@ -78,7 +78,6 @@ subroutine ice_write_hist (ns)
       character (char_len) :: title
       character (char_len) :: time_period_freq = 'none'
       character (char_len_long) :: ncfile(max_nstrm)
-      integer (kind=int_kind) :: iotype
 
       integer (kind=int_kind) :: icategory,ind,i_aice,boundid
 
@@ -167,11 +166,9 @@ subroutine ice_write_hist (ns)
       call broadcast_scalar(filename, master_task)
 
       ! create file
-      iotype = PIO_IOTYPE_NETCDF
-      if (history_format == 'pio_pnetcdf') iotype = PIO_IOTYPE_PNETCDF
       File%fh=-1
       call ice_pio_init(mode='write', filename=trim(filename), File=File, &
-        clobber=.true., cdf64=lcdf64, iotype=iotype)
+        clobber=.true., fformat=trim(history_format))
 
       call ice_pio_initdecomp(iodesc=iodesc2d, precision=history_precision)
       call ice_pio_initdecomp(ndim3=ncat_hist, iodesc=iodesc3dc, precision=history_precision)
@@ -741,13 +738,8 @@ subroutine ice_write_hist (ns)
       call ice_pio_check(pio_put_att(File,pio_global,'history',trim(start_time)), &
            subname//' ERROR: defining att history '//trim(start_time),file=__FILE__,line=__LINE__)
 
-      if (history_format == 'pio_pnetcdf') then
-         call ice_pio_check(pio_put_att(File,pio_global,'io_flavor','io_pio pnetcdf'), &
-              subname//' ERROR: defining att io_flavor',file=__FILE__,line=__LINE__)
-      else
-         call ice_pio_check(pio_put_att(File,pio_global,'io_flavor','io_pio netcdf'), &
-              subname//' ERROR: defining att io_flavor',file=__FILE__,line=__LINE__)
-      endif
+      call ice_pio_check(pio_put_att(File,pio_global,'io_flavor','io_pio '//trim(history_format)), &
+           subname//' ERROR: defining att io_flavor',file=__FILE__,line=__LINE__)
 
       !-----------------------------------------------------------------
       ! end define mode

cicecore/cicedyn/infrastructure/io/io_pio2/ice_pio.F90

@@ -44,7 +44,7 @@ module ice_pio
 !    Initialize the io subsystem
 !    2009-Feb-17 - J. Edwards - initial version
 
-   subroutine ice_pio_init(mode, filename, File, clobber, cdf64, iotype)
+   subroutine ice_pio_init(mode, filename, File, clobber, fformat)
 
 #ifdef CESMCOUPLED
    use shr_pio_mod, only: shr_pio_getiosys, shr_pio_getiotype
@@ -59,16 +59,16 @@ subroutine ice_pio_init(mode, filename, File, clobber, cdf64, iotype)
    character(len=*)     , intent(in),    optional :: filename
    type(file_desc_t)    , intent(inout), optional :: File
    logical              , intent(in),    optional :: clobber
-   logical              , intent(in),    optional :: cdf64
-   integer              , intent(in),    optional :: iotype
+   character(len=*)     , intent(in),    optional :: fformat
 
    ! local variables
 
    integer (int_kind) :: &
       nml_error          ! namelist read error flag
 
-   integer :: nprocs , istride, basetask, numiotasks, rearranger, pio_iotype, status, nmode
-   logical :: lclobber, lcdf64, exists
+   integer :: nprocs , istride, basetask, numiotasks, rearranger
+   integer ::pio_iotype, status, nmode0, nmode
+   logical :: lclobber, exists
    logical, save :: first_call = .true.
    character(len=*), parameter :: subname = '(ice_pio_init)'
 
@@ -86,12 +86,26 @@ subroutine ice_pio_init(mode, filename, File, clobber, cdf64, iotype)
 #endif
 
    !--- initialize type of io
-   !pio_iotype = PIO_IOTYPE_PNETCDF
-   !pio_iotype = PIO_IOTYPE_NETCDF4C
-   !pio_iotype = PIO_IOTYPE_NETCDF4P
-   pio_iotype = PIO_IOTYPE_NETCDF
-   if (present(iotype)) then
-      pio_iotype = iotype
+
+   lclobber = .false.
+   if (present(clobber)) lclobber=clobber
+
+   if (fformat(1:3) == 'cdf') then
+     pio_iotype = PIO_IOTYPE_NETCDF
+   elseif (fformat(1:3) == 'hdf') then
+     pio_iotype = PIO_IOTYPE_NETCDF4P 
+   elseif (fformat(1:7) == 'pnetcdf') then
+     pio_iotype = PIO_IOTYPE_PNETCDF
+   else
+     call abort_ice(subname//' ERROR: format not allowed for '//trim(fformat), &
+        file=__FILE__, line=__LINE__)
+   endif
+
+   nmode0 = 0
+   if (fformat == 'cdf2' .or. fformat == 'pnetcdf2') then
+      nmode0 = PIO_64BIT_OFFSET
+   elseif (fformat == 'cdf5' .or. fformat == 'pnetcdf5') then
+      nmode0 = PIO_64BIT_DATA
    endif
 
    !--- initialize ice_pio_subsystem
@@ -102,12 +116,14 @@ subroutine ice_pio_init(mode, filename, File, clobber, cdf64, iotype)
 !--tcraig this should work better but it causes pio2.4.4 to fail for reasons unknown
 !   numiotasks = 1 + (nprocs-basetask-1)/istride
    rearranger = PIO_REARR_BOX
+
    if (my_task == master_task) then
       write(nu_diag,*) subname,' nprocs     = ',nprocs
       write(nu_diag,*) subname,' istride    = ',istride
       write(nu_diag,*) subname,' basetask   = ',basetask
       write(nu_diag,*) subname,' numiotasks = ',numiotasks
       write(nu_diag,*) subname,' pio_iotype = ',pio_iotype
+      write(nu_diag,*) subname,' nmode      = ',nmode0
    end if
 
    call pio_init(my_task, MPI_COMM_ICE, numiotasks, master_task, istride, &
@@ -139,19 +155,13 @@ subroutine ice_pio_init(mode, filename, File, clobber, cdf64, iotype)
    if (present(mode) .and. present(filename) .and. present(File)) then
 
       if (trim(mode) == 'write') then
-         lclobber = .false.
-         if (present(clobber)) lclobber=clobber
-
-         lcdf64 = .false.
-         if (present(cdf64)) lcdf64=cdf64
 
          if (File%fh<0) then
             ! filename not open
             inquire(file=trim(filename),exist=exists)
             if (exists) then
                if (lclobber) then
-                  nmode = pio_clobber
-                  if (lcdf64) nmode = ior(nmode,PIO_64BIT_OFFSET)
+                  nmode = ior(PIO_CLOBBER,nmode0)
                   status = pio_createfile(ice_pio_subsystem, File, pio_iotype, trim(filename), nmode)
                   call ice_pio_check(status, subname//' ERROR: Failed to create file '//trim(filename), &
                        file=__FILE__,line=__LINE__)
@@ -168,8 +178,7 @@ subroutine ice_pio_init(mode, filename, File, clobber, cdf64, iotype)
                   end if
                endif
             else
-               nmode = pio_noclobber
-               if (lcdf64) nmode = ior(nmode,PIO_64BIT_OFFSET)
+               nmode = ior(PIO_NOCLOBBER,nmode0)
                status = pio_createfile(ice_pio_subsystem, File, pio_iotype, trim(filename), nmode)
                call ice_pio_check( status, subname//' ERROR: Failed to create file '//trim(filename), &
                     file=__FILE__,line=__LINE__)