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Use optional chunksizes argument in register_restart_field calls (#595)
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* Change the format of domain restart files to netcdf4 and set chunksizes

* Remove nc_format="netcdf4" argument when opening restart files

* Set chunksize of zaxis and time axis to 1

* Update clm_lake and rrfs_sd modules to support chunksizes

* Make quilting restart files identical to fms files
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@DusanJovic-NOAA
DusanJovic-NOAA authored Aug 31, 2023
1 parent 51e570c commit d9525db
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Showing 6 changed files with 94 additions and 53 deletions.
2 changes: 1 addition & 1 deletion atmos_cubed_sphere
Submodule atmos_cubed_sphere updated 1 files
+68 −21 tools/fv_io.F90
64 changes: 36 additions & 28 deletions io/fv3atm_clm_lake_io.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ module fv3atm_clm_lake_io
use block_control_mod, only: block_control_type
use fms2_io_mod, only: FmsNetcdfDomainFile_t, register_axis, &
register_restart_field, write_data, &
register_variable_attribute, register_field
register_variable_attribute, register_field, get_dimension_size
use fv3atm_common_io, only: create_2d_field_and_add_to_bundle, &
create_3d_field_and_add_to_bundle

Expand Down Expand Up @@ -370,81 +370,89 @@ subroutine clm_lake_register_fields(clm_lake, Sfc_restart)
class(clm_lake_data_type) :: clm_lake
type(FmsNetcdfDomainFile_t) :: Sfc_restart

integer :: xaxis_1_chunk, yaxis_1_chunk
integer :: chunksizes2d(3), chunksizes3d(4)

call get_dimension_size(Sfc_restart, 'xaxis_1', xaxis_1_chunk)
call get_dimension_size(Sfc_restart, 'yaxis_1', yaxis_1_chunk)
chunksizes2d = (/xaxis_1_chunk, yaxis_1_chunk, 1/)
chunksizes3d = (/xaxis_1_chunk, yaxis_1_chunk, 1, 1/)

! Register 2D fields
call register_restart_field(Sfc_restart, 'T_snow', clm_lake%T_snow, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'T_ice', clm_lake%T_ice, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'lake_snl2d', clm_lake%lake_snl2d, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'lake_h2osno2d', clm_lake%lake_h2osno2d, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'lake_tsfc', clm_lake%lake_tsfc, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'lake_savedtke12d', clm_lake%lake_savedtke12d, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'lake_sndpth2d', clm_lake%lake_sndpth2d, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'clm_lakedepth', clm_lake%clm_lakedepth, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'clm_lake_initialized', clm_lake%clm_lake_initialized, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)

! Register 3D fields
call register_restart_field(Sfc_restart, 'lake_z3d', clm_lake%lake_z3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levlake_clm_lake ', 'Time '/), is_optional=.true.)
'levlake_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'lake_dz3d', clm_lake%lake_dz3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levlake_clm_lake ', 'Time '/), is_optional=.true.)
'levlake_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_soil_watsat3d', clm_lake%lake_soil_watsat3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levlake_clm_lake ', 'Time '/), is_optional=.true.)
'levlake_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_csol3d', clm_lake%lake_csol3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levlake_clm_lake ', 'Time '/), is_optional=.true.)
'levlake_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_soil_tkmg3d', clm_lake%lake_soil_tkmg3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levlake_clm_lake ', 'Time '/), is_optional=.true.)
'levlake_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_soil_tkdry3d', clm_lake%lake_soil_tkdry3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levlake_clm_lake ', 'Time '/), is_optional=.true.)
'levlake_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_soil_tksatu3d', clm_lake%lake_soil_tksatu3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levlake_clm_lake ', 'Time '/), is_optional=.true.)
'levlake_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_snow_z3d', clm_lake%lake_snow_z3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levsnowsoil1_clm_lake', 'Time '/), is_optional=.true.)
'levsnowsoil1_clm_lake', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_snow_dz3d', clm_lake%lake_snow_dz3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levsnowsoil1_clm_lake', 'Time '/), is_optional=.true.)
'levsnowsoil1_clm_lake', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_snow_zi3d', clm_lake%lake_snow_zi3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levsnowsoil_clm_lake ', 'Time '/), is_optional=.true.)
'levsnowsoil_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_h2osoi_vol3d', clm_lake%lake_h2osoi_vol3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levsnowsoil1_clm_lake', 'Time '/), is_optional=.true.)
'levsnowsoil1_clm_lake', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_h2osoi_liq3d', clm_lake%lake_h2osoi_liq3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levsnowsoil1_clm_lake', 'Time '/), is_optional=.true.)
'levsnowsoil1_clm_lake', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_h2osoi_ice3d', clm_lake%lake_h2osoi_ice3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levsnowsoil1_clm_lake', 'Time '/), is_optional=.true.)
'levsnowsoil1_clm_lake', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_t_soisno3d', clm_lake%lake_t_soisno3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levsnowsoil1_clm_lake', 'Time '/), is_optional=.true.)
'levsnowsoil1_clm_lake', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_t_lake3d', clm_lake%lake_t_lake3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levlake_clm_lake ', 'Time '/), is_optional=.true.)
'levlake_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_icefrac3d', clm_lake%lake_icefrac3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levlake_clm_lake ', 'Time '/), is_optional=.true.)
'levlake_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_clay3d', clm_lake%lake_clay3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levsoil_clm_lake ', 'Time '/), is_optional=.true.)
'levsoil_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
call register_restart_field(Sfc_restart,'lake_sand3d', clm_lake%lake_sand3d, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'levsoil_clm_lake ', 'Time '/), is_optional=.true.)
'levsoil_clm_lake ', 'Time '/), chunksizes=chunksizes3d, is_optional=.true.)
end subroutine clm_lake_register_fields

!>@ This is clm_lake%bundle_fields, and it is only used in the
Expand Down
9 changes: 6 additions & 3 deletions io/fv3atm_restart_io.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ module fv3atm_restart_io_mod
register_axis, register_restart_field, &
register_variable_attribute, register_field, &
read_restart, write_restart, write_data, &
get_global_io_domain_indices
get_global_io_domain_indices, get_dimension_size
use mpp_domains_mod, only: domain2d
use fv3atm_common_io, only: create_2d_field_and_add_to_bundle, &
create_3d_field_and_add_to_bundle, copy_from_gfs_data
Expand Down Expand Up @@ -891,6 +891,7 @@ subroutine phys_restart_write (GFS_Restart, Atm_block, Model, fv_domain, timesta
character(7) :: indir='RESTART'
character(72) :: infile
logical :: amiopen, allocated_something
integer :: xaxis_1_chunk, yaxis_1_chunk

type(phy_data_type) :: phy
type(FmsNetcdfDomainFile_t) :: Phy_restart
Expand All @@ -917,13 +918,15 @@ subroutine phys_restart_write (GFS_Restart, Atm_block, Model, fv_domain, timesta
call get_global_io_domain_indices(Phy_restart, 'xaxis_1', is, ie, indices=buffer)
call write_data(Phy_restart, "xaxis_1", buffer)
deallocate(buffer)
call get_dimension_size(Phy_restart, 'xaxis_1', xaxis_1_chunk)

call register_axis(Phy_restart, 'yaxis_1', 'Y')
call register_field(Phy_restart, 'yaxis_1', 'double', (/'yaxis_1'/))
call register_variable_attribute(Phy_restart, 'yaxis_1', 'cartesian_axis', 'Y', str_len=1)
call get_global_io_domain_indices(Phy_restart, 'yaxis_1', is, ie, indices=buffer)
call write_data(Phy_restart, "yaxis_1", buffer)
deallocate(buffer)
call get_dimension_size(Phy_restart, 'yaxis_1', yaxis_1_chunk)

call register_axis(Phy_restart, 'zaxis_1', phy%npz)
call register_field(Phy_restart, 'zaxis_1', 'double', (/'zaxis_1'/))
Expand All @@ -946,12 +949,12 @@ subroutine phys_restart_write (GFS_Restart, Atm_block, Model, fv_domain, timesta
do num = 1,phy%nvar2d
var2_p => phy%var2(:,:,num)
call register_restart_field(Phy_restart, trim(GFS_Restart%name2d(num)), var2_p, dimensions=(/'xaxis_1','yaxis_1','Time '/),&
&is_optional=.true.)
& chunksizes=(/xaxis_1_chunk,yaxis_1_chunk,1/), is_optional=.true.)
enddo
do num = 1,phy%nvar3d
var3_p => phy%var3(:,:,:,num)
call register_restart_field(Phy_restart, trim(GFS_Restart%name3d(num)), var3_p, dimensions=(/'xaxis_1','yaxis_1','zaxis_1','Time '/),&
&is_optional=.true.)
& chunksizes=(/xaxis_1_chunk,yaxis_1_chunk,1,1/), is_optional=.true.)
enddo
nullify(var2_p)
nullify(var3_p)
Expand Down
23 changes: 16 additions & 7 deletions io/fv3atm_rrfs_sd_io.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@ module fv3atm_rrfs_sd_io
use block_control_mod, only: block_control_type
use fms2_io_mod, only: FmsNetcdfDomainFile_t, write_data, &
register_axis, register_restart_field, &
register_variable_attribute, register_field
register_variable_attribute, register_field, &
get_dimension_size
use GFS_typedefs, only: GFS_sfcprop_type, GFS_control_type, kind_phys
use fv3atm_common_io, only: get_nx_ny_from_atm, create_2d_field_and_add_to_bundle, &
create_3d_field_and_add_to_bundle
Expand Down Expand Up @@ -193,23 +194,31 @@ subroutine rrfs_sd_state_register_fields(data,Sfc_restart)
class(rrfs_sd_state_type) :: data
type(FmsNetcdfDomainFile_t) :: Sfc_restart

integer :: xaxis_1_chunk, yaxis_1_chunk
integer :: chunksizes2d(3), chunksizes3d(4)

call get_dimension_size(Sfc_restart, 'xaxis_1', xaxis_1_chunk)
call get_dimension_size(Sfc_restart, 'yaxis_1', yaxis_1_chunk)
chunksizes2d = (/xaxis_1_chunk, yaxis_1_chunk, 1/)
chunksizes3d = (/xaxis_1_chunk, yaxis_1_chunk, 1, 1/)

! Register 2D fields
call register_restart_field(Sfc_restart, 'emdust', data%emdust, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'emseas', data%emseas, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'emanoc', data%emanoc, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'fhist', data%fhist, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)
call register_restart_field(Sfc_restart, 'coef_bb_dc', data%coef_bb_dc, &
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), is_optional=.true.)
dimensions=(/'xaxis_1', 'yaxis_1', 'Time '/), chunksizes=chunksizes2d, is_optional=.true.)

! Register 3D field
call register_restart_field(Sfc_restart, 'fire_in', data%fire_in, &
dimensions=(/'xaxis_1 ', 'yaxis_1 ', &
'fire_aux_data_levels', 'Time '/), &
is_optional=.true.)
chunksizes=chunksizes3d, is_optional=.true.)
end subroutine rrfs_sd_state_register_fields

! --------------------------------------------------------------------
Expand Down
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