From d12390015c9a0664f6ceab5695d06bc814998711 Mon Sep 17 00:00:00 2001 From: Uriel Ramirez Date: Mon, 7 Aug 2023 12:59:40 -0400 Subject: [PATCH 1/2] add the write_data calls --- diag_manager/Makefile.am | 2 +- diag_manager/fms_diag_file_object.F90 | 37 ++++++++- diag_manager/fms_diag_object.F90 | 4 +- diag_manager/fms_diag_output_buffer.F90 | 101 +++++++++++++++++++++++- 4 files changed, 138 insertions(+), 6 deletions(-) diff --git a/diag_manager/Makefile.am b/diag_manager/Makefile.am index b5570cf5ff..4933350e6f 100644 --- a/diag_manager/Makefile.am +++ b/diag_manager/Makefile.am @@ -87,7 +87,7 @@ diag_manager_mod.$(FC_MODEXT): diag_axis_mod.$(FC_MODEXT) diag_data_mod.$(FC_MOD fms_diag_object_container_mod.$(FC_MODEXT) fms_diag_axis_object_mod.$(FC_MODEXT) \ fms_diag_time_reduction_mod.$(FC_MODEXT) fms_diag_outfield_mod.$(FC_MODEXT) \ fms_diag_fieldbuff_update_mod.$(FC_MODEXT) -fms_diag_output_buffer_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) +fms_diag_output_buffer_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) fms_diag_yaml_mod.$(FC_MODEXT) # Mod files are built and then installed as headers. MODFILES = \ diff --git a/diag_manager/fms_diag_file_object.F90 b/diag_manager/fms_diag_file_object.F90 index 5a277971e6..7d4a457391 100644 --- a/diag_manager/fms_diag_file_object.F90 +++ b/diag_manager/fms_diag_file_object.F90 @@ -45,7 +45,7 @@ module fms_diag_file_object_mod fmsDiagFullAxis_type, define_subaxis, define_diurnal_axis, & fmsDiagDiurnalAxis_type, create_new_z_subaxis use fms_diag_field_object_mod, only: fmsDiagField_type -use fms_diag_output_buffer_mod, only: fmsDiagOutputBufferContainer_type +use fms_diag_output_buffer_mod, only: fmsDiagOutputBufferContainer_type, fmsDiagOutputBuffer_class use mpp_mod, only: mpp_get_current_pelist, mpp_npes, mpp_root_pe, mpp_pe, mpp_error, FATAL, stdout, & uppercase, lowercase @@ -161,6 +161,7 @@ module fms_diag_file_object_mod procedure :: open_diag_file procedure :: write_global_metadata procedure :: write_time_metadata + procedure :: write_field_data procedure :: write_axis_metadata procedure :: write_field_metadata procedure :: write_axis_data @@ -1119,6 +1120,40 @@ subroutine write_time_metadata(this) end subroutine write_time_metadata +!> \brief Write out the field data to the file +subroutine write_field_data(this, field_obj, buffer_obj) + class(fmsDiagFileContainer_type), intent(in), target :: this !< The file object + type(fmsDiagField_type), intent(in), target :: field_obj(:) + type(fmsDiagOutputBufferContainer_type), intent(in), target :: buffer_obj(:) + + class(fmsDiagFile_type), pointer :: diag_file !< Diag_file object to open + class(FmsNetcdfFile_t), pointer :: fileobj !< Fileobj to write to + integer :: i !< For do loops + integer :: field_id !< The id of the field writing the data to + + diag_file => this%FMS_diag_file + fileobj => diag_file%fileobj + + if (diag_file%is_static) then + !< Here the file is static so there is no need for the unlimited dimension + !! as a variables are static + do i = 1, diag_file%number_of_buffers + call buffer_obj(diag_file%buffer_ids(i))%write_buffer(fileobj) + enddo + else + do i = 1, diag_file%number_of_buffers + field_id = buffer_obj(diag_file%buffer_ids(i))%get_field_id() + if (field_obj(field_id)%is_static()) then + !< If the variable is static, only write it the first time + if (diag_file%unlim_dimension_level .eq. 1) call buffer_obj(diag_file%buffer_ids(i))%write_buffer(fileobj) + else + call buffer_obj(diag_file%buffer_ids(i))%write_buffer(fileobj, unlim_dim_level=diag_file%unlim_dimension_level) + endif + enddo + endif + +end subroutine write_field_data + !> \brief Determine if it is time to close the file !! \return .True. if it is time to close the file logical function is_time_to_close_file (this, time_step) diff --git a/diag_manager/fms_diag_object.F90 b/diag_manager/fms_diag_object.F90 index 46099be45c..5915a604e0 100644 --- a/diag_manager/fms_diag_object.F90 +++ b/diag_manager/fms_diag_object.F90 @@ -227,7 +227,7 @@ integer function fms_register_diag_field_obj & fieldptr%buffer_ids = get_diag_field_ids(diag_field_indices) do i = 1, size(fieldptr%buffer_ids) call this%FMS_diag_output_buffers(fieldptr%buffer_ids(i))%set_field_id(this%registered_variables) - call this%FMS_diag_output_buffers(fieldptr%buffer_ids(i))%set_yaml_id(diag_field_indices(i)) + call this%FMS_diag_output_buffers(fieldptr%buffer_ids(i))%set_yaml_id(fieldptr%buffer_ids(i)) enddo !> Allocate and initialize member buffer_allocated of this field @@ -719,7 +719,7 @@ subroutine fms_diag_do_io(this, is_end_of_run) if (diag_file%is_time_to_write(model_time)) then call diag_file%increase_unlim_dimension_level() call diag_file%write_time_data() - !TODO call diag_file%add_variable_data() + call diag_file%write_field_data(this%FMS_diag_fields, this%FMS_diag_output_buffers) call diag_file%update_next_write(model_time) call diag_file%update_current_new_file_freq_index(model_time) if (diag_file%is_time_to_close_file(model_time)) call diag_file%close_diag_file() diff --git a/diag_manager/fms_diag_output_buffer.F90 b/diag_manager/fms_diag_output_buffer.F90 index 3603bb4321..4820e84da1 100644 --- a/diag_manager/fms_diag_output_buffer.F90 +++ b/diag_manager/fms_diag_output_buffer.F90 @@ -24,18 +24,19 @@ !! buffer0-5d types extend fmsDiagBuffer_class, and upon allocation !! are added to the module's buffer_lists depending on it's dimension module fms_diag_output_buffer_mod - +#ifdef use_yaml use platform_mod use iso_c_binding use time_manager_mod, only: time_type use mpp_mod, only: mpp_error, FATAL use diag_data_mod, only: DIAG_NULL, DIAG_NOT_REGISTERED, i4, i8, r4, r8 +use fms2_io_mod, only: FmsNetcdfFile_t, write_data, FmsNetcdfDomainFile_t, FmsNetcdfUnstructuredDomainFile_t +use fms_diag_yaml_mod, only: diag_yaml implicit none private -#ifdef use_yaml !> @brief Object that holds buffered data and other diagnostics !! Abstract to ensure use through its extensions(buffer0-5d types) type, abstract :: fmsDiagOutputBuffer_class @@ -72,6 +73,11 @@ module fms_diag_output_buffer_mod procedure :: get_field_id procedure :: set_yaml_id procedure :: get_yaml_id + procedure :: write_buffer + !! These are needed because otherwise the write_data calls will go into the wrong interface + procedure :: write_buffer_wrapper_netcdf + procedure :: write_buffer_wrapper_domain + procedure :: write_buffer_wrapper_u end type !> Scalar buffer type to extend fmsDiagBufferContainer_type @@ -1497,5 +1503,96 @@ function get_yaml_id(this) & res = this%yaml_id end function get_yaml_id + +!> @brief Write the buffer to the file +subroutine write_buffer(this, fileobj, unlim_dim_level) + class(fmsDiagOutputBufferContainer_type), intent(in) :: this !< buffer object to write + class(FmsNetcdfFile_t), intent(in) :: fileobj !< fileobj to write to + integer, optional, intent(in) :: unlim_dim_level !< unlimited dimension + + select type(fileobj) + type is (FmsNetcdfFile_t) + call this%write_buffer_wrapper_netcdf(fileobj, unlim_dim_level=unlim_dim_level) + type is (FmsNetcdfDomainFile_t) + call this%write_buffer_wrapper_domain(fileobj, unlim_dim_level=unlim_dim_level) + type is (FmsNetcdfUnstructuredDomainFile_t) + call this%write_buffer_wrapper_u(fileobj, unlim_dim_level=unlim_dim_level) + end select +end subroutine write_buffer + +!> @brief Write the buffer to the FmsNetcdfFile_t fileobj +subroutine write_buffer_wrapper_netcdf(this, fileobj, unlim_dim_level) + class(fmsDiagOutputBufferContainer_type), intent(in) :: this !< buffer object to write + type(FmsNetcdfFile_t), intent(in) :: fileobj !< fileobj to write to + integer, optional, intent(in) :: unlim_dim_level !< unlimited dimension + + character(len=:), allocatable :: varname !< name of the variable + + varname = diag_yaml%diag_fields(this%yaml_id)%get_var_outname() + select type(buffer_obj=>this%diag_buffer_obj) + type is (outputBuffer0d_type) + call write_data(fileobj, varname, buffer_obj%buffer(1), unlim_dim_level=unlim_dim_level) + type is (outputBuffer1d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer2d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer3d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer4d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer5d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + end select +end subroutine + +!> @brief Write the buffer to the FmsNetcdfDomainFile_t fileobj +subroutine write_buffer_wrapper_domain(this, fileobj, unlim_dim_level) + class(fmsDiagOutputBufferContainer_type), intent(in) :: this !< buffer object to write + type(FmsNetcdfDomainFile_t), intent(in) :: fileobj !< fileobj to write to + integer, optional, intent(in) :: unlim_dim_level !< unlimited dimension + + character(len=:), allocatable :: varname !< name of the variable + + varname = diag_yaml%diag_fields(this%yaml_id)%get_var_outname() + select type(buffer_obj=>this%diag_buffer_obj) + type is (outputBuffer0d_type) + call write_data(fileobj, varname, buffer_obj%buffer(1), unlim_dim_level=unlim_dim_level) + type is (outputBuffer1d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer2d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer3d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer4d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer5d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + end select +end subroutine + +!> @brief Write the buffer to the FmsNetcdfUnstructuredDomainFile_t fileobj +subroutine write_buffer_wrapper_u(this, fileobj, unlim_dim_level) + class(fmsDiagOutputBufferContainer_type), intent(in) :: this !< buffer object to write + type(FmsNetcdfUnstructuredDomainFile_t), intent(in) :: fileobj !< fileobj to write to + integer, optional, intent(in) :: unlim_dim_level !< unlimited dimension + + character(len=:), allocatable :: varname !< name of the variable + + varname = diag_yaml%diag_fields(this%yaml_id)%get_var_outname() + select type(buffer_obj=>this%diag_buffer_obj) + type is (outputBuffer0d_type) + call write_data(fileobj, varname, buffer_obj%buffer(1), unlim_dim_level=unlim_dim_level) + type is (outputBuffer1d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer2d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer3d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer4d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + type is (outputBuffer5d_type) + call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + end select +end subroutine #endif end module fms_diag_output_buffer_mod From e6b86a46e360bf4008840583efddbfbf2465f752 Mon Sep 17 00:00:00 2001 From: Uriel Ramirez Date: Thu, 10 Aug 2023 08:36:23 -0400 Subject: [PATCH 2/2] Add additional error checking + fix the test_flexible_time after the update + minor documentation updates --- diag_manager/fms_diag_file_object.F90 | 9 +++++---- diag_manager/fms_diag_output_buffer.F90 | 18 +++++++++++++++--- test_fms/diag_manager/test_flexible_time.F90 | 18 +++++++++++++----- 3 files changed, 33 insertions(+), 12 deletions(-) diff --git a/diag_manager/fms_diag_file_object.F90 b/diag_manager/fms_diag_file_object.F90 index 7d4a457391..84c3f3980e 100644 --- a/diag_manager/fms_diag_file_object.F90 +++ b/diag_manager/fms_diag_file_object.F90 @@ -1122,18 +1122,19 @@ end subroutine write_time_metadata !> \brief Write out the field data to the file subroutine write_field_data(this, field_obj, buffer_obj) - class(fmsDiagFileContainer_type), intent(in), target :: this !< The file object - type(fmsDiagField_type), intent(in), target :: field_obj(:) - type(fmsDiagOutputBufferContainer_type), intent(in), target :: buffer_obj(:) + class(fmsDiagFileContainer_type), intent(in), target :: this !< The diag file object to write to + type(fmsDiagField_type), intent(in), target :: field_obj(:) !< The field object to write from + type(fmsDiagOutputBufferContainer_type), intent(in), target :: buffer_obj(:) !< The buffer object with the data class(fmsDiagFile_type), pointer :: diag_file !< Diag_file object to open class(FmsNetcdfFile_t), pointer :: fileobj !< Fileobj to write to integer :: i !< For do loops - integer :: field_id !< The id of the field writing the data to + integer :: field_id !< The id of the field writing the data from diag_file => this%FMS_diag_file fileobj => diag_file%fileobj + !TODO This may be offloaded in the future if (diag_file%is_static) then !< Here the file is static so there is no need for the unlimited dimension !! as a variables are static diff --git a/diag_manager/fms_diag_output_buffer.F90 b/diag_manager/fms_diag_output_buffer.F90 index 4820e84da1..3f2e1db095 100644 --- a/diag_manager/fms_diag_output_buffer.F90 +++ b/diag_manager/fms_diag_output_buffer.F90 @@ -1517,6 +1517,9 @@ subroutine write_buffer(this, fileobj, unlim_dim_level) call this%write_buffer_wrapper_domain(fileobj, unlim_dim_level=unlim_dim_level) type is (FmsNetcdfUnstructuredDomainFile_t) call this%write_buffer_wrapper_u(fileobj, unlim_dim_level=unlim_dim_level) + class default + call mpp_error(FATAL, "The file "//trim(fileobj%path)//" is not one of the accepted types"//& + " only FmsNetcdfFile_t, FmsNetcdfDomainFile_t, and FmsNetcdfUnstructuredDomainFile_t are accepted.") end select end subroutine write_buffer @@ -1542,8 +1545,11 @@ subroutine write_buffer_wrapper_netcdf(this, fileobj, unlim_dim_level) call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) type is (outputBuffer5d_type) call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + class default + call mpp_error(FATAL, "The field:"//trim(varname)//" does not have a valid buffer object type."//& + " Only 0d, 1d, 2d, 3d, 4d, and 5d buffers are supported.") end select -end subroutine +end subroutine write_buffer_wrapper_netcdf !> @brief Write the buffer to the FmsNetcdfDomainFile_t fileobj subroutine write_buffer_wrapper_domain(this, fileobj, unlim_dim_level) @@ -1567,8 +1573,11 @@ subroutine write_buffer_wrapper_domain(this, fileobj, unlim_dim_level) call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) type is (outputBuffer5d_type) call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + class default + call mpp_error(FATAL, "The field:"//trim(varname)//" does not have a valid buffer object type."//& + " Only 0d, 1d, 2d, 3d, 4d, and 5d buffers are supported.") end select -end subroutine +end subroutine write_buffer_wrapper_domain !> @brief Write the buffer to the FmsNetcdfUnstructuredDomainFile_t fileobj subroutine write_buffer_wrapper_u(this, fileobj, unlim_dim_level) @@ -1592,7 +1601,10 @@ subroutine write_buffer_wrapper_u(this, fileobj, unlim_dim_level) call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) type is (outputBuffer5d_type) call write_data(fileobj, varname, buffer_obj%buffer, unlim_dim_level=unlim_dim_level) + class default + call mpp_error(FATAL, "The field:"//trim(varname)//" does not have a valid buffer object type."//& + " Only 0d, 1d, 2d, 3d, 4d, and 5d buffers are supported.") end select -end subroutine +end subroutine write_buffer_wrapper_u #endif end module fms_diag_output_buffer_mod diff --git a/test_fms/diag_manager/test_flexible_time.F90 b/test_fms/diag_manager/test_flexible_time.F90 index a3a78a5f8f..2dd881177d 100644 --- a/test_fms/diag_manager/test_flexible_time.F90 +++ b/test_fms/diag_manager/test_flexible_time.F90 @@ -21,15 +21,19 @@ program test_flexible_time use fms_mod, only: fms_init, fms_end use time_manager_mod, only: set_date, time_type, increment_date, set_calendar_type, & - JULIAN, set_time + JULIAN, set_time, operator(+) use diag_manager_mod, only: diag_manager_init, diag_axis_init, register_diag_field, & - diag_manager_set_time_end, diag_send_complete, diag_manager_end + diag_manager_set_time_end, diag_send_complete, diag_manager_end, & + send_data use mpp_mod, only: FATAL, mpp_error +use platform_mod, only: r8_kind implicit none +real(kind=r8_kind) :: var_data(2) !< Dummy data +logical :: used !< .True. if send_data was sucessful type(time_type) :: Time !< Time of the simulation -type(time_type) :: Start_Time !< Start time of the simulation +type(time_type) :: Time_step !< Start time of the simulation type(time_type) :: End_Time !< End Time of the simulation integer :: i integer :: id_z, id_var @@ -39,18 +43,22 @@ program test_flexible_time call diag_manager_init !< Starting time of the simulation -Start_Time = set_date(2,1,1,3,0,0) !02/01/01 hour 3 +Time = set_date(2,1,1,3,0,0) !02/01/01 hour 3 !< Set up a dummy variable id_z = diag_axis_init('z', (/1. ,2. /), 'point_Z', 'z', long_name='point_Z') -id_var = register_diag_field ('atm_mod', 'var1', (/id_z/), Start_Time, 'Var not domain decomposed', 'mullions') +id_var = register_diag_field ('atm_mod', 'var1', (/id_z/), Time, 'Var not domain decomposed', 'mullions') !< Set up the end of the simulation (i.e 2 days long) End_Time = set_date(2,1,3,3,0,0) call diag_manager_set_time_end(End_Time) !< Set up the simulation +Time_step = set_time (3600,0) !< 1 hour do i=1,48 + var_data = real(i, kind=r8_kind) + Time = Time + Time_step + used = send_data(id_var, var_data, Time) call diag_send_complete(set_time(3600,0)) enddo