obs_diag

Running obs_diag on CAM output

Change directory to the case’s run directory:

$ cd /lustre/scratch/x_johnsobk/FHIST_BGC.f09_d025.104.e0250/run

Echo a list of all of the obs_seq.final files into a text file:

$ ls -d -1 "$PWD/"\*final\*00000\* > /lustre/project/k1421/DART/models/cam-fv/work/obs_seq_final_list.txt

Change directory to DART’s CAM-FV work directory:

$ cd /lustre/project/k1421/DART/models/cam-fv/work/

Edit the &obs_diag_nml namelist in input.nml to reflect our experimental configuration:

&obs_diag_nml
   obs_sequence_name = ''
   obs_sequence_list = 'obs_seq_final_list.txt'
   first_bin_center =  2019, 8, 6, 12, 0, 0
   last_bin_center  =  2019, 8, 18, 12, 0, 0
   bin_separation   =     0, 0, 1, 0, 0, 0
   bin_width        =     0, 0, 1, 0, 0, 0
   time_to_skip     =     0, 0, 0, 0, 0, 0
   max_num_bins     = 1000
   trusted_obs      = 'null'
   plevel_edges = 1036.5, 962.5, 887.5, 775, 600, 450, 350, 275, 225,   175,   125,   75,   35,   15,    2
   hlevel_edges =    200, 630,   930,  1880,3670,5680,7440,9130,10530,12290, 14650,18220,23560,29490,43000
   Nregions   = 3
   lonlim1    =   0.0,   0.0,   0.0
   lonlim2    = 360.0, 360.0, 360.0
   latlim1    =  20.0, -20.0, -90.0
   latlim2    =  90.0,  20.0, -20.0
   reg_names  = 'Northern Hemisphere', 'Tropics', 'Southern Hemisphere'
   print_mismatched_locs = .false.
   create_rank_histogram = .true.
   outliers_in_histogram = .true.
   use_zero_error_obs    = .false.
   verbose               = .false.
/

Since Shaheen doesn’t seem to be able to run the Fortran executables from the login nodes, we need to make a batch script to submit that merely just runs obs_diag.

$ vim run_obs_diag.csh

#!/bin/csh

#SBATCH --job-name=run_obs_diag
#SBATCH --account=k1421
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=00:59:00
#SBATCH --partition=workq
#SBATCH --output=run_obs_diag.out.%j

./obs_diag

exit 0

Submit the script we just created and wait for it to complete. It will create a file named obs_diag_output.nc.

$ sbatch run_obs_diag.csh
[...]
$ ls -lart
obs_diag_output.nc

Using the MATLAB Diagnostic Scripts

Now that we have obs_diag_output.nc, we can use the MATLAB diagnostic scripts to see statistics about the ensemble. Navigate to the DART sub-directory containing the diagnostic scripts and start MATLAB.

$ mv obs_diag_output.nc $DARTROOT/diagnostics/matlab
$ cd $DARTROOT/diagnostics/matlab
$ matlab

Once MATLAB is open, run plot_evolution.m using:

>> fname   = 'obs_diag_output.nc';
>> copy    = 'bias';
>> plotdat = plot_evolution(fname, copy);

This will output a slew of diagnostic plots.