[Dart-dev] DART/branches Revision: 12486

[dart at ucar.edu]

nancy at ucar.edu
2018-04-03 14:11:22 -0600 (Tue, 03 Apr 2018)
208
we probably don't want all these changes; some are already
on the rma_trunk.  but commit everything to this branch
so i can diff it with the rma_trunk and see what never
got reviewed and moved that we want.




Modified: DART/branches/rma_updates_nancy/assimilation_code/modules/assimilation/filter_mod.f90
===================================================================
--- DART/branches/rma_updates_nancy/assimilation_code/modules/assimilation/filter_mod.f90	2018-04-03 17:05:54 UTC (rev 12485)
+++ DART/branches/rma_updates_nancy/assimilation_code/modules/assimilation/filter_mod.f90	2018-04-03 20:11:22 UTC (rev 12486)
@@ -173,7 +173,8 @@
 logical  :: output_timestamps        = .false.
 logical  :: trace_execution          = .false.
 logical  :: silence                  = .false.
-logical  :: distributed_state = .true. ! Default to do state complete forward operators.
+logical  :: distributed_state        = .true. ! Default is RMA mode: state complete FOs
+logical  :: write_partial_obs_seq_for_debug = .false.
 
 ! IO options
 ! Names of files given explicitly in namelist
@@ -249,7 +250,8 @@
    stages_to_write, &
    input_state_files, output_state_files, &
    output_state_file_list, input_state_file_list, &
-   output_mean, output_sd, write_all_stages_at_end
+   output_mean, output_sd, write_all_stages_at_end, &
+   write_partial_obs_seq_for_debug 
 
 
 !----------------------------------------------------------------
@@ -820,8 +822,7 @@
 
    call trace_message('Before observation space diagnostics')
 
-   ! This is where the mean obs
-   ! copy ( + others ) is moved to task 0 so task 0 can update seq.
+   ! This is where the mean obs copy ( + others ) is moved to task 0 so it can update seq.
    ! There is a transpose (all_copies_to_all_vars(obs_fwd_op_ens_handle)) in obs_space_diagnostics
    ! Do prior observation space diagnostics and associated quality control
    call obs_space_diagnostics(obs_fwd_op_ens_handle, qc_ens_handle, ens_size, &
@@ -966,7 +967,7 @@
 
    call trace_message('Before posterior obs space diagnostics')
 
-   ! Write posterior observation space diagnostics
+   ! This is where the mean obs copy ( + others ) is moved to task 0 so it can update seq.
    ! There is a transpose (all_copies_to_all_vars(obs_fwd_op_ens_handle)) in obs_space_diagnostics
    call obs_space_diagnostics(obs_fwd_op_ens_handle, qc_ens_handle, ens_size, &
       seq, keys, POSTERIOR_DIAG, num_output_obs_members, in_obs_copy+2, &
@@ -975,9 +976,19 @@
       OBS_MEAN_START, OBS_VAR_START, OBS_GLOBAL_QC_COPY, &
       OBS_VAL_COPY, OBS_ERR_VAR_COPY, DART_qc_index)
 
-
    call trace_message('After  posterior obs space diagnostics')
 
+   ! this costs time and only runs on task 0. it should only be set to true if
+   ! filter is crashing before execution finishes and you want to see what the
+   ! obs_seq file looks like so far.  the full file will be written at the normal
+   ! end of execution.
+   if (write_partial_obs_seq_for_debug) then
+      call trace_message('Before writing partial output sequence file for debug')
+      ! Only pe 0 outputs the observation space diagnostic file
+      if(my_task_id() == 0) call write_obs_seq(seq, obs_sequence_out_name)
+      call trace_message('After  writing partial output sequence file for debug')
+   endif
+
    ! this block computes the adaptive state space posterior inflation
    ! (it was applied earlier, this is computing the updated values for
    ! the next cycle.)

Modified: DART/branches/rma_updates_nancy/assimilation_code/modules/io/state_vector_io_mod.f90
===================================================================
--- DART/branches/rma_updates_nancy/assimilation_code/modules/io/state_vector_io_mod.f90	2018-04-03 17:05:54 UTC (rev 12485)
+++ DART/branches/rma_updates_nancy/assimilation_code/modules/io/state_vector_io_mod.f90	2018-04-03 20:11:22 UTC (rev 12486)
@@ -73,6 +73,8 @@
 use single_file_io_mod, only : init_singlefile_output, write_singlefile, &
                                  read_singlefile
 
+!use assim_tools_mod, only : get_missing_ok_status
+
 use netcdf
 
 
@@ -288,6 +290,8 @@
 integer :: domain     ! loop index
 type(stage_metadata_type) :: restart_files
 
+real(r8) :: clm_missing = 1e+36
+
 ! check whether file_info handle is initialized
 call assert_file_info_initialized(file_info, 'read_restart_direct')
 
@@ -310,6 +314,11 @@
 
 ! Need Temporary print of initial model time?
 
+!! a semi-hack for the CLM missing values in state mess.
+!if (get_missing_ok_status()) then
+!   where(state_ens_handle%copies == clm_missing) state_ens_handle%copies = MISSING_R8
+!endif
+
 end subroutine read_restart_direct
 
 
@@ -325,6 +334,8 @@
 integer :: dart_index !< where to start in state_ens_handle%copies