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reducing post-processing of XIOS output #204

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a59cab6
lfric_xios: move time, convention and description out of post process…
mo-marqh Dec 1, 2025
4ed0042
file format version consistent with lfric_apps - fragile
mo-marqh Dec 2, 2025
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55 changes: 39 additions & 16 deletions components/lfric-xios/source/lfric_xios_context_mod.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,9 @@ module lfric_xios_context_mod
use field_mod, only : field_type
use file_mod, only : file_type
use io_context_mod, only : io_context_type, callback_clock_arg
use io_config_mod, only : file_convention, &
file_convention_ugrid, &
file_convention_cf
use lfric_xios_file_mod, only : lfric_xios_file_type
use lfric_mpi_mod, only : lfric_comm_type
use log_mod, only : log_event, log_scratch_space, &
Expand All @@ -24,6 +27,7 @@ module lfric_xios_context_mod
setup_xios_files
use lfric_xios_file_mod, only : lfric_xios_file_type
use linked_list_mod, only : linked_list_type, linked_list_item_type
use mesh_mod, only : mesh_type
use model_clock_mod, only : model_clock_type
use timer_mod, only : timer
use xios, only : xios_context, &
Expand All @@ -49,6 +53,9 @@ module lfric_xios_context_mod

logical :: uses_timer = .false.
logical :: xios_context_initialised = .false.
!> Flag denoting if this file is a UGRID Planar mesh file with
!> projected coordinates that have been scaled
logical :: ugrid_scaled_projected_coordinates = .false.

contains
private
Expand Down Expand Up @@ -112,6 +119,7 @@ subroutine initialise_xios_context( this, communicator, &
type(field_type), optional, intent(in) :: alt_panel_ids(:)
logical, optional, intent(in) :: start_at_zero

type(mesh_type), pointer :: mesh => null()
type(linked_list_item_type), pointer :: loop => null()
type(lfric_xios_file_type), pointer :: file => null()
logical :: zero_start
Expand All @@ -133,8 +141,17 @@ subroutine initialise_xios_context( this, communicator, &

! Run XIOS setup routines
call init_xios_calendar(model_clock, calendar, zero_start, this%context_clock_step)

call init_xios_dimensions(chi, panel_id, alt_coords, alt_panel_ids)
if (this%filelist%get_length() > 0) call setup_xios_files(this%filelist)
! Obtain information on whether the mesh is ugrid and planar here?
! This is to inform decisions on file post processing work around code path.
mesh => chi(1)%get_mesh()
if ( mesh%is_geometry_planar() .and. &
file_convention == file_convention_ugrid ) then
this%ugrid_scaled_projected_coordinates = .true.
end if
if (this%filelist%get_length() > 0) call setup_xios_files(this%filelist, &
this%ugrid_scaled_projected_coordinates)

if (associated(before_close)) call before_close(model_clock)

Expand Down Expand Up @@ -197,22 +214,28 @@ subroutine finalise_xios_context( this )
call log_event(log_scratch_space, log_level_debug)
call xios_context_finalize()

! We have closed the context on our end, but we need to make sure that XIOS
! has closed the files for all servers before we process them.
call init_wait()

! Close all files in list
if (this%filelist%get_length() > 0) then
loop => this%filelist%get_head()
do while (associated(loop))
select type( list_item => loop%payload )
type is (lfric_xios_file_type)
file => list_item
call file%file_close()
end select
loop => loop%next
end do
! Only take action if this is a regional model with UGRID Projected
! coordinates, as these are awaiting XIOS feature development
if ( this%ugrid_scaled_projected_coordinates ) then
call log_event("Closing file for post processing.", LOG_LEVEL_DEBUG)
! We have closed the context on our end, but we need to make sure that XIOS
! has closed the files for all servers before we process them.
call init_wait()

! Close all files in list
if (this%filelist%get_length() > 0) then
loop => this%filelist%get_head()
do while (associated(loop))
select type( list_item => loop%payload )
type is (lfric_xios_file_type)
file => list_item
call file%file_close()
end select
loop => loop%next
end do
end if
end if

this%xios_context_initialised = .false.
end if
nullify(loop)
Expand Down
31 changes: 27 additions & 4 deletions components/lfric-xios/source/lfric_xios_file_mod.f90
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Expand Up @@ -89,6 +89,9 @@ module lfric_xios_file_mod
logical :: is_diag = .false.
!> Flag denoting if the always-on sampling mode is selected
logical :: diag_always_on_sampling = .true.
!> Flag denoting if this file is a UGRID Planar mesh file with
!> projected coordinates that have been scaled
logical :: ugrid_scaled_projected_coordinates = .false.
!> Will the file be read again from the beginning once the end is reached
logical :: cyclic = .false.
!>
Expand Down Expand Up @@ -116,6 +119,7 @@ module lfric_xios_file_mod
procedure, public :: mode_is_write
procedure, public :: recv_fields
procedure, public :: send_fields
procedure, public :: set_ugrid_scaled_projected_coordinates
final :: lfric_xios_file_final

end type lfric_xios_file_type
Expand Down Expand Up @@ -312,10 +316,16 @@ subroutine file_close(self)
if (self%is_closed) return

if ( self%io_mode == FILE_MODE_WRITE ) then
call log_event( "Waiting for XIOS to close file ["//trim(self%path)//".nc]", &
log_level_debug )
call init_wait()
call process_output_file(trim(self%path)//".nc")
! Only take action if this is a regional model with UGRID Projected
! coordinates, as these are awaiting XIOS feature development
if ( self%ugrid_scaled_projected_coordinates ) then
call log_event( "Waiting for XIOS to close file ["//trim(self%path)//".nc]", &
log_level_debug )
call init_wait()
call log_event( "post processing file ["//trim(self%path)//".nc]", &
log_level_debug )
call process_output_file(trim(self%path)//".nc")
end if
end if

self%is_closed = .true.
Expand Down Expand Up @@ -570,4 +580,17 @@ subroutine lfric_xios_file_final(self)

end subroutine lfric_xios_file_final

!> @brief Setter for the file object ugrid_scaled_projected_coordinates
!> @param[in] ugrid_scaled_projected_coordinates Logical
!>
subroutine set_ugrid_scaled_projected_coordinates(self, ugrid_scaled_projected_coordinates)

implicit none
logical, intent(in) :: ugrid_scaled_projected_coordinates
class(lfric_xios_file_type), intent(inout) :: self

self%ugrid_scaled_projected_coordinates = ugrid_scaled_projected_coordinates

end subroutine set_ugrid_scaled_projected_coordinates

end module lfric_xios_file_mod
138 changes: 18 additions & 120 deletions components/lfric-xios/source/lfric_xios_process_output_mod.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,13 @@
! under which the code may be used.
!-------------------------------------------------------------------------------

!> @brief Module to hold routines for processing XIOS output for compliance
!> with downstream data requirements
!> @brief Module to only hold routines for re-processing files output by XIOS
!> where the configuration is unable to be delivered by XIOS.
!> The only facet in scope for this module is post processing projected
!> coordinates for UGRId specification files, pending new feature
!> development in XIOS. This is technical debt, and this
!> post processing approach should not be used for other file
!> manipulations.
!>
module lfric_xios_process_output_mod

Expand All @@ -21,24 +26,21 @@ module lfric_xios_process_output_mod
use lfric_ncdf_field_group_mod, only: lfric_ncdf_field_group_type
use lfric_ncdf_file_mod, only: lfric_ncdf_file_type
use lfric_xios_constants_mod, only: dp_xios
use lfric_xios_utils_mod, only: parse_date_as_xios, seconds_from_date
use log_mod, only: log_event, log_level_trace
use xios, only: xios_date, xios_get_start_date
use log_mod, only: log_event, log_level_trace, &
log_level_info

implicit none

public :: process_output_file, set_xios_geometry_planar
public :: process_output_file
private

! Public scaling factor for planar mesh coordinates to circumvent XIOS issue
real(kind=dp_xios), public, parameter :: xyz_scaling_factor = 1.0e-4_dp_xios

logical :: model_has_planar_geometry = .false.

contains

!> @brief Processes a NetCDF file produced by XIOS to align with the LFRic
!! UGRID file format
!> @brief Processes a NetCDF file produced by XIOS to work around
!> limmitations in UGRID projected coordinates only.
!>
!> @param[in] file_path The path to the NetCDF file to be edited
subroutine process_output_file(file_path)
Expand All @@ -53,7 +55,7 @@ subroutine process_output_file(file_path)
! Output processing must be done in serial
if (global_mpi%get_comm_rank() /= 0) return

call log_event("Processing output file: "//trim(file_path), log_level_trace)
call log_event("Processing output file: "//trim(file_path), log_level_info)

! If file has not been written out, then don't attempt to process it
inquire(file=trim(file_path), exist=file_exists)
Expand All @@ -64,41 +66,14 @@ subroutine process_output_file(file_path)
open_mode=FILE_OP_OPEN, &
io_mode=FILE_MODE_WRITE )

call format_version(file_ncdf)

if (file_convention == file_convention_ugrid) then
call format_mesh(file_ncdf)
end if

call format_time(file_ncdf)

call file_ncdf%close_file()

end subroutine process_output_file

!> @brief Tags output file with the current version number of the LFRic file
!! format
!>
!> @param[in] file_ncdf The netcdf file to be edited
subroutine format_version(file_ncdf)

implicit none

type(lfric_ncdf_file_type), intent(inout) :: file_ncdf

call file_ncdf%set_attribute("description", "LFRic file format v0.2.0")

select case(file_convention)
case (file_convention_ugrid)
call file_ncdf%set_attribute("Conventions", "UGRID-1.0")

case (file_convention_cf)
call file_ncdf%set_attribute("Conventions", "CF")

end select

end subroutine format_version

!> @brief Formats the mesh object in the output file
!>
!> @param[in] file_ncdf The netcdf file to be edited
Expand All @@ -114,83 +89,15 @@ subroutine format_mesh(file_ncdf)

mesh_var = lfric_ncdf_field_type("Mesh2d", file_ncdf)

if (model_has_planar_geometry) then
call mesh_var%set_char_attribute("geometry", "planar")
call fix_planar_coordinates(file_ncdf)
else
call mesh_var%set_char_attribute("geometry", "spherical")
end if
! This post process code should only be called on a file where
! the model has Planar geometry and is UGRID encoded.
! This is controlled by lfric_xios_context_mod,
! lfric_xios_file_mod and lfric_xios_setup_mod
call fix_planar_coordinates(file_ncdf)

end subroutine format_mesh


!> @brief Formats the time coordinate into CF compliant forecast metadata
!>
!> @param[in] file_ncdf The netcdf file to be edited
subroutine format_time(output_file)

implicit none

type(lfric_ncdf_file_type), intent(in) :: output_file
! In the future we may need an optional argument to determine the expected
! name of the time axis

type(lfric_ncdf_dims_type) :: time_dims
type(lfric_ncdf_field_type) :: time_field, frt_field, fp_field
type(lfric_ncdf_field_group_type) :: fields_in_file, time_var_fields
type(xios_date) :: time_origin_date, model_start_date
character(:), allocatable :: time_var_name, time_dim_name
real(r_def), allocatable :: time_data(:), fp(:)
real(r_def) :: frt(1)
integer(i_def) :: i

! Set time variable and dimension names
time_var_name = "time"
time_dim_name = "time"

! Files that contain no time-variation will not have a time
! variable/dimension, so they do not need to be processed
if (.not. output_file%contains_var(trim(time_var_name))) return

! Read the time data from the output file
time_field = lfric_ncdf_field_type(trim(time_var_name), output_file)
time_dims = lfric_ncdf_dims_type(trim(time_dim_name), output_file)
allocate(time_data(time_dims%get_size()))
call time_field%read_data(time_data)

! Calculate forecast metadata using XIOS calendar
time_origin_date = parse_date_as_xios( &
trim(adjustl(time_field%get_char_attribute("time_origin"))) )
call xios_get_start_date(model_start_date)
frt(1) = seconds_from_date(model_start_date) - &
seconds_from_date(time_origin_date)

allocate(fp(time_dims%get_size()))
do i = 1, time_dims%get_size()
fp(i) = time_data(i) - seconds_from_date(time_origin_date)
end do

! Setup netCDF fields for forecast metadata
frt_field = lfric_ncdf_field_type("forecast_reference_time", output_file)
call frt_field%write_data(frt)
call frt_field%set_char_attribute("units", "seconds since "// &
trim(adjustl(time_field%get_char_attribute("time_origin"))))
call frt_field%set_char_attribute("calendar", time_field%get_char_attribute("calendar"))
call frt_field%set_char_attribute("standard_name", "forecast_reference_time")

fp_field = lfric_ncdf_field_type("forecast_period", output_file, time_dims)
call fp_field%write_data(fp)
call fp_field%set_char_attribute("units", "seconds")
call fp_field%set_char_attribute("standard_name", "forecast_period")

! Set forecast metadata as time coordinates
fields_in_file = lfric_ncdf_field_group_type(output_file, output_file%get_all_varids())
time_var_fields = fields_in_file%get_group_subset(dimension=time_dims)
call time_var_fields%add_coordinate("forecast_reference_time")
call time_var_fields%add_coordinate("forecast_period")

end subroutine format_time

!> @brief Fixes issues with planar coordinates in output file
!>
!> @param[in] file_ncdf The netcdf file to be edited
Expand Down Expand Up @@ -224,13 +131,4 @@ subroutine fix_planar_coordinates(file_ncdf)

end subroutine fix_planar_coordinates

!> @brief Specifies that the model is running on a mesh with planar geometry
subroutine set_xios_geometry_planar()

implicit none

model_has_planar_geometry = .true.

end subroutine set_xios_geometry_planar

end module lfric_xios_process_output_mod
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