implement flush_nc_files in the new diag manager and adds a test

diag_manager/fms_diag_file_object.F90

@@ -28,13 +28,14 @@ module fms_diag_file_object_mod
 use fms2_io_mod, only: FmsNetcdfFile_t, FmsNetcdfUnstructuredDomainFile_t, FmsNetcdfDomainFile_t, &
                        get_instance_filename, open_file, close_file, get_mosaic_tile_file, unlimited, &
                        register_axis, register_field, register_variable_attribute, write_data, &
-                       dimension_exists, register_global_attribute
+                       dimension_exists, register_global_attribute, flush_file
 use diag_data_mod, only: DIAG_NULL, NO_DOMAIN, max_axes, SUB_REGIONAL, get_base_time, DIAG_NOT_REGISTERED, &
                          TWO_D_DOMAIN, UG_DOMAIN, prepend_date, DIAG_DAYS, VERY_LARGE_FILE_FREQ, &
                          get_base_year, get_base_month, get_base_day, get_base_hour, get_base_minute, &
                          get_base_second, time_unit_list, time_average, time_rms, time_max, time_min, time_sum, &
                          time_diurnal, time_power, time_none, avg_name, no_units, pack_size_str, &
-                         middle_time, begin_time, end_time, MAX_STR_LEN, index_gridtype, latlon_gridtype, null_gridtype
+                         middle_time, begin_time, end_time, MAX_STR_LEN, index_gridtype, latlon_gridtype, &
+                         null_gridtype, flush_nc_files
 use time_manager_mod, only: time_type, operator(>), operator(/=), operator(==), get_date, get_calendar_type, &
                             VALID_CALENDAR_TYPES, operator(>=), date_to_string, &
                             OPERATOR(/), OPERATOR(+), operator(<)
@@ -192,6 +193,7 @@ module fms_diag_file_object_mod
   procedure :: init_unlim_dim
   procedure :: update_current_new_file_freq_index
   procedure :: get_unlim_dimension_level
+  procedure :: flush_diag_file
   procedure :: get_next_output
   procedure :: get_next_next_output
   procedure :: close_diag_file
@@ -1591,6 +1593,15 @@ pure function get_unlim_dimension_level(this) &
   res = this%FMS_diag_file%unlim_dimension_level
 end function
 
+!> \brief Flushes the netcdf file to disk if flush_nc_files is set to .True. in the namelist
+subroutine flush_diag_file(this)
+  class(fmsDiagFileContainer_type), intent(inout), target   :: this            !< The file object
+
+  if (flush_nc_files) then
+    call flush_file(this%FMS_diag_file%fms2io_fileobj)
+  endif
+end subroutine flush_diag_file
+
 !> \brief Get the next_output for the file object
 !! \return The next_output
 pure function get_next_output(this) &

diag_manager/fms_diag_object.F90

@@ -873,6 +873,7 @@ subroutine fms_diag_do_io(this, end_time)
 
     if (unlim_dim_was_increased) then
       call diag_file%write_time_data()
+      call diag_file%flush_diag_file()
       call diag_file%update_next_write(model_time)
     endif
 

test_fms/diag_manager/Makefile.am

@@ -29,7 +29,7 @@ LDADD = $(top_builddir)/libFMS/libFMS.la
 
 # Build this test program.
 check_PROGRAMS = test_diag_manager test_diag_manager_time \
- test_diag_yaml test_diag_ocean test_modern_diag test_diag_buffer \
+ test_diag_yaml test_diag_ocean test_modern_diag test_diag_buffer test_flush_nc_file\
  test_flexible_time test_diag_update_buffer test_reduction_methods check_time_none \
  check_time_min check_time_max check_time_sum check_time_avg test_diag_diurnal check_time_diurnal \
  check_time_pow check_time_rms check_subregional test_cell_measures test_var_masks \
@@ -47,6 +47,7 @@ test_diag_ocean_SOURCES = test_diag_ocean.F90
 test_modern_diag_SOURCES = test_modern_diag.F90
 test_diag_buffer_SOURCES= test_diag_buffer.F90
 test_flexible_time_SOURCES = test_flexible_time.F90
+test_flush_nc_file_SOURCES = test_flush_nc_file.F90
 test_diag_out_yaml_SOURCES = test_diag_out_yaml.F90
 test_reduction_methods_SOURCES = testing_utils.F90 test_reduction_methods.F90
 test_diag_diurnal_SOURCES = testing_utils.F90 test_diag_diurnal.F90
@@ -72,15 +73,15 @@ SH_LOG_DRIVER = env AM_TAP_AWK='$(AWK)' $(SHELL) \
 TESTS = test_diag_manager2.sh test_time_none.sh test_time_min.sh test_time_max.sh test_time_sum.sh \
         test_time_avg.sh test_time_pow.sh test_time_rms.sh test_time_diurnal.sh test_cell_measures.sh \
         test_subregional.sh test_var_masks.sh test_multiple_send_data.sh test_output_every_freq.sh \
-        test_dm_weights.sh
+        test_dm_weights.sh test_flush_nc_file.sh
 
 testing_utils.mod: testing_utils.$(OBJEXT)
 
 # Copy over other needed files to the srcdir
 EXTRA_DIST = test_diag_manager2.sh check_crashes.sh test_time_none.sh test_time_min.sh test_time_max.sh \
              test_time_sum.sh test_time_avg.sh test_time_pow.sh test_time_rms.sh test_time_diurnal.sh \
              test_cell_measures.sh test_subregional.sh test_var_masks.sh test_multiple_send_data.sh \
-             test_dm_weights.sh test_output_every_freq.sh
+             test_flush_nc_file.sh test_dm_weights.sh test_output_every_freq.sh
 
 if USING_YAML
 skipflag=""

test_fms/diag_manager/test_flush_nc_file.F90

@@ -0,0 +1,108 @@
+!***********************************************************************
+!*                   GNU Lesser General Public License
+!*
+!* This file is part of the GFDL Flexible Modeling System (FMS).
+!*
+!* FMS is free software: you can redistribute it and/or modify it under
+!* the terms of the GNU Lesser General Public License as published by
+!* the Free Software Foundation, either version 3 of the License, or (at
+!* your option) any later version.
+!*
+!* FMS is distributed in the hope that it will be useful, but WITHOUT
+!* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+!* FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+!* for more details.
+!*
+!* You should have received a copy of the GNU Lesser General Public
+!* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
+!***********************************************************************
+
+!> @brief  This programs tests when flush_nc_file=.true.
+program test_flush_nc_file
+  use fms_mod, only: fms_init, fms_end
+  use diag_manager_mod
+  use mpp_mod
+  use mpp_domains_mod
+  use platform_mod,     only: r8_kind, r4_kind
+  use time_manager_mod, only: time_type, set_calendar_type, set_date, JULIAN, set_time, OPERATOR(+)
+  use fms2_io_mod
+  use fms_diag_yaml_mod
+
+  implicit none
+
+  type(time_type)                    :: Time             !< Time of the simulation
+  type(time_type)                    :: Time_step        !< Time_step of the simulation
+  integer                            :: nx               !< Number of x points
+  integer                            :: ny               !< Number of y points
+  integer                            :: nz               !< Number of z points
+  integer                            :: id_x             !< Axis id for the x dimension
+  integer                            :: id_y             !< Axis id for the y dimension
+  integer                            :: id_var1          !< Field id for 1st variable
+  logical                            :: used             !< Dummy argument to send_data
+  real,                  allocatable :: x(:)             !< X axis data
+  real,                  allocatable :: y(:)             !< Y axis_data
+  real,                  allocatable :: var1_data(:,:)   !< Data for variable 1
+  integer                            :: i                !< For do loops
+
+  call fms_init
+  call set_calendar_type(JULIAN)
+  call diag_manager_init
+
+  nx = 360
+  ny = 180
+
+  allocate(x(nx), y(ny))
+  allocate(var1_data(nx,ny))
+  do i=1,nx
+    x(i) = i
+  enddo
+  do i=1,ny
+    y(i) = -91 + i
+  enddo
+
+  Time = set_date(2,1,1,0,0,0)
+  Time_step = set_time (3600,0) !< 1 hour
+
+  id_x  = diag_axis_init('x',  x,  'point_E', 'x', long_name='point_E')
+  id_y  = diag_axis_init('y',  y,  'point_N', 'y', long_name='point_N')
+  id_var1 = register_diag_field  ('atmos', 'ua', (/id_x, id_y/), Time)
+
+  call diag_manager_set_time_end(set_date(2,1,2,0,0,0))
+  do i = 1, 24
+    Time = Time + Time_step
+    var1_data = real(i)
+    used = send_data(id_var1, var1_data, Time)
+    if (mpp_pe() .eq. mpp_root_pe()) print *, "Calling send_data::", i
+    call diag_send_complete(Time_step)
+    call mpp_sync()
+    ! The file should have been flushed by now
+    call check_answers(i)
+  enddo
+
+  call diag_manager_end(Time)
+  !call check_answers(i)
+  call fms_end
+
+  contains
+    subroutine check_answers(time_level)
+      integer, intent(in) :: time_level
+      type(FmsNetcdfFile_t) :: fileobj
+      integer                            :: ntimes
+      real,   allocatable                :: vardata(:,:)
+
+      if (mpp_pe() .ne. mpp_root_pe()) return
+      if (.not. open_file(fileobj, "test_flush.nc", "read")) &
+        call mpp_error(FATAL, "unable to open test_flush.nc for reading")
+
+      call get_dimension_size(fileobj, "time", ntimes)
+      if (ntimes .ne. time_level) call mpp_error(FATAL, "time is not the correct size::", time_level)
+
+      allocate(vardata(nx,ny))
+
+      call read_data(fileobj, "ua", vardata, unlim_dim_level=i)
+      if (any(vardata .ne. time_level)) &
+        call mpp_error(FATAL, "ua is not the expected result")
+
+      call close_file(fileobj)
+    end subroutine check_answers
+end program test_flush_nc_file

test_fms/diag_manager/test_flush_nc_file.sh

@@ -0,0 +1,53 @@
+#!/bin/sh
+
+#***********************************************************************
+#*                   GNU Lesser General Public License
+#*
+#* This file is part of the GFDL Flexible Modeling System (FMS).
+#*
+#* FMS is free software: you can redistribute it and/or modify it under
+#* the terms of the GNU Lesser General Public License as published by
+#* the Free Software Foundation, either version 3 of the License, or (at
+#* your option) any later version.
+#*
+#* FMS is distributed in the hope that it will be useful, but WITHOUT
+#* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+#* FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+#* for more details.
+#*
+#* You should have received a copy of the GNU Lesser General Public
+#* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
+#***********************************************************************
+
+# Set common test settings.
+. ../test-lib.sh
+
+if [ -z "${skipflag}" ]; then
+# create and enter directory for in/output files
+output_dir
+
+cat <<_EOF > diag_table.yaml
+title: test_nc_flush
+base_date: 2 1 1 0 0 0
+diag_files:
+- file_name: test_flush
+  time_units: hours
+  unlimdim: time
+  freq: 1 hours
+  varlist:
+  - module: atmos
+    var_name: ua
+    reduction: average
+    kind: r4
+_EOF
+
+# remove any existing files that would result in false passes during checks
+rm -f *.nc
+
+my_test_count=1
+printf "&diag_manager_nml \n use_modern_diag=.true. \n flush_nc_files=.true. \n/" | cat > input.nml
+test_expect_success "Running diag_manager with flush_nc_files = .true. (test $my_test_count)" '
+  mpirun -n 1 ../test_var_masks
+'
+fi
+test_done