Have the driver script process both python scripts and YAMLs + bufr2ioda.x by CoryMartin-NOAA · Pull Request #730 · NOAA-EMC/GDASApp

CoryMartin-NOAA · 2023-11-15T17:26:02Z

This PR allows for all obtypes to be processed in two loops.

We still need to figure out a way to process these in parallel (somewhat).

CoryMartin-NOAA · 2023-11-15T17:26:33Z

Coding norms are failing, I will fix this after my meeting(s)

RussTreadon-NOAA

Test proposed changes in JEDI gdas-validation. 2021080100 gdasprepatmiodaobs aborted with the following traceback

2023-11-15 18:38:52,983 - INFO     - run_bufr2ioda.py: Executing /work2/noaa/da/rtreadon/gdas-validation/global-workflow/sorc/gdas.cd/build/bin/bufr2ioda.x /work2/noaa/da/rtreadon/gdas-validation/comrot/gdas_eval_satwind_JEDI/gdas.20210801/00/obs/atms_2021080100.yaml
PRE-MAIN-INFO BufrParser: Parsing file /work/noaa/rstprod/dump/gdas.20210801/00/atmos/gdas.t00z.atms.tm00.bufr_d
PRE-MAIN-INFO Executing Queries
PRE-MAIN-INFO Building Bufr Data
PRE-MAIN-INFO Exporting Data
 ATMS_Spatial_Average: chechking bt_inout (original) ...
 minval/maxval bt_inout (original) =    133.0100       310.3900
 Unable to open atms_beamwidth.txt
PRE-MAIN-ERROR Exception: Bad parameter: Missing required parameters: sensor. Check your configuration.
terminate called after throwing an instance of 'eckit::BadParameter'
  what():  Bad parameter: Missing required parameters: sensor. Check your configuration.
Traceback (most recent call last):
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/run_bufr2ioda.py", line 94, in <module>
    bufr2ioda(args.current_cycle, args.RUN, args.DMPDIR, args.config_template_dir, args.COM_OBS)
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/python/wxflow/logger.py", line 266, in wrapper
    retval = func(*args, **kwargs)
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/run_bufr2ioda.py", line 79, in bufr2ioda
    cmd()
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/python/wxflow/executable.py", line 230, in __call__
    raise ProcessError(f"Command exited with status {proc.returncode}:", long_msg)
wxflow.executable.ProcessError: Command exited with status -6:
'/work2/noaa/da/rtreadon/gdas-validation/global-workflow/sorc/gdas.cd/build/bin/bufr2ioda.x' '/work2/noaa/da/rtreadon/gdas-validation/comrot/gdas_eval_satwind_JEDI/gdas.20210801/00/obs/atms_2021080100.yaml'

Not sure if this is due to my set up or an issue with the proposed changes. Investigating.

CoryMartin-NOAA · 2023-11-15T18:48:00Z

@RussTreadon-NOAA I get the same error now in testing, let me investigate

RussTreadon-NOAA · 2023-11-15T18:54:32Z

atms_beamwidth.txt1 is referenced in

iodaconv/src/bufr/BufrParser/Exports/Variables/Transforms/atms/atms_spatial_average_mod.f90:    open(lninfile,file='atms_beamwidth.txt',form='formatted',status='old', &
iodaconv/src/bufr/BufrParser/Exports/Variables/Transforms/atms/atms_spatial_average_mod.f90:       write(*,*) 'Unable to open atms_beamwidth.txt'
iodaconv/src/bufr/BufrParser/Exports/Variables/Transforms/atms/atms_spatial_average_mod.f90:       write(*,*) 'ATMS_Spatial_Averaging: sat id not matched in atms_beamwidth.dat'

We have atms_beamwidth.txt in GSI fix. Would copying it to the prepatmiodaobs run directory be sufficient?

CoryMartin-NOAA · 2023-11-15T19:00:26Z

@RussTreadon-NOAA yeah I think so, now I just need to figure out how best to copy it to the runtime directory.

RussTreadon-NOAA · 2023-11-15T19:01:42Z

Add the following to jobs/JGLOBAL_ATM_PREP_IODA_OBS

##TEST
cp ${HOMEgfs}/fix/gsi/atms_beamwidth.txt $DATA/
##TEST

before executing run_bufr2ioda.py. Rewind and reboot gdasprepatmiodaobs.

RussTreadon-NOAA · 2023-11-15T19:10:32Z

Copying atm_beamwidth.txt to $DATA helped, but prepatmiodaobs still bombed.

2023-11-15 19:05:43,229 - INFO     - run_bufr2ioda.py: Executing /work2/noaa/da/rtreadon/gdas-validation/global-workflow/sorc/gdas.cd/build/bin/bufr2ioda.x /work2/noaa/da/rtreadon/gdas-validation/comrot/gdas_eval_satwind_JEDI/gdas.20210801/00/obs/atms_2021080100.yaml
PRE-MAIN-INFO BufrParser: Parsing file /work/noaa/rstprod/dump/gdas.20210801/00/atmos/gdas.t00z.atms.tm00.bufr_d
PRE-MAIN-INFO Executing Queries
PRE-MAIN-INFO Building Bufr Data
PRE-MAIN-INFO Exporting Data
 ATMS_Spatial_Average: chechking bt_inout (original) ...
 minval/maxval bt_inout (original) =    133.0100       310.3900
 ATMS_Spatial_Average: minval/maxval scanline =            1        8100
 ATMS_Spatial_Average: chechking bt_inout (remapped) ...
 minval/maxval bt_inout (remapped) =    127.9957      9.9999998E+10
PRE-MAIN-ERROR Exception: Bad parameter: Missing required parameters: sensor. Check your configuration.
terminate called after throwing an instance of 'eckit::BadParameter'
  what():  Bad parameter: Missing required parameters: sensor. Check your configuration.
Traceback (most recent call last):
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/run_bufr2ioda.py", line 94, in <module>
    bufr2ioda(args.current_cycle, args.RUN, args.DMPDIR, args.config_template_dir, args.COM_OBS)
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/python/wxflow/logger.py", line 266, in wrapper
    retval = func(*args, **kwargs)
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/run_bufr2ioda.py", line 79, in bufr2ioda
    cmd()
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/python/wxflow/executable.py", line 230, in __call__
    raise ProcessError(f"Command exited with status {proc.returncode}:", long_msg)
wxflow.executable.ProcessError: Command exited with status -6:
'/work2/noaa/da/rtreadon/gdas-validation/global-workflow/sorc/gdas.cd/build/bin/bufr2ioda.x' '/work2/noaa/da/rtreadon/gdas-validation/comrot/gdas_eval_satwind_JEDI/gdas.20210801/00/obs/atms_2021080100.yaml'

Required parameter sensor missing.

Who developed the atms converter? How did they test it?

FYI, we need to increase the wall time for prepatmiodaobs. 10 minutes is no longer sufficient. Later we can refactor prepatmiodaobs to concurrently run multiple converters via CFP

CoryMartin-NOAA · 2023-11-15T19:12:27Z

@emilyhcliu is going to look into it

CoryMartin-NOAA · 2023-11-15T19:39:06Z

I think I know the issue, I'm testing now, (it's a one liner)

emilyhcliu · 2023-11-15T19:40:17Z

Copying atm_beamwidth.txt to $DATA helped, but prepatmiodaobs still bombed.

2023-11-15 19:05:43,229 - INFO     - run_bufr2ioda.py: Executing /work2/noaa/da/rtreadon/gdas-validation/global-workflow/sorc/gdas.cd/build/bin/bufr2ioda.x /work2/noaa/da/rtreadon/gdas-validation/comrot/gdas_eval_satwind_JEDI/gdas.20210801/00/obs/atms_2021080100.yaml
PRE-MAIN-INFO BufrParser: Parsing file /work/noaa/rstprod/dump/gdas.20210801/00/atmos/gdas.t00z.atms.tm00.bufr_d
PRE-MAIN-INFO Executing Queries
PRE-MAIN-INFO Building Bufr Data
PRE-MAIN-INFO Exporting Data
 ATMS_Spatial_Average: chechking bt_inout (original) ...
 minval/maxval bt_inout (original) =    133.0100       310.3900
 ATMS_Spatial_Average: minval/maxval scanline =            1        8100
 ATMS_Spatial_Average: chechking bt_inout (remapped) ...
 minval/maxval bt_inout (remapped) =    127.9957      9.9999998E+10
PRE-MAIN-ERROR Exception: Bad parameter: Missing required parameters: sensor. Check your configuration.
terminate called after throwing an instance of 'eckit::BadParameter'
  what():  Bad parameter: Missing required parameters: sensor. Check your configuration.
Traceback (most recent call last):
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/run_bufr2ioda.py", line 94, in <module>
    bufr2ioda(args.current_cycle, args.RUN, args.DMPDIR, args.config_template_dir, args.COM_OBS)
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/python/wxflow/logger.py", line 266, in wrapper
    retval = func(*args, **kwargs)
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/run_bufr2ioda.py", line 79, in bufr2ioda
    cmd()
  File "/work2/noaa/da/rtreadon/gdas-validation/global-workflow/ush/python/wxflow/executable.py", line 230, in __call__
    raise ProcessError(f"Command exited with status {proc.returncode}:", long_msg)
wxflow.executable.ProcessError: Command exited with status -6:
'/work2/noaa/da/rtreadon/gdas-validation/global-workflow/sorc/gdas.cd/build/bin/bufr2ioda.x' '/work2/noaa/da/rtreadon/gdas-validation/comrot/gdas_eval_satwind_JEDI/gdas.20210801/00/obs/atms_2021080100.yaml'

Required parameter sensor missing.

Who developed the atms converter? How did they test it?

FYI, we need to increase the wall time for prepatmiodaobs. 10 minutes is no longer sufficient. Later we can refactor prepatmiodaobs to concurrently run multiple converters via CFP

Yes, @RussTreadon-NOAA I will take over and test ATMS with the changes in this PR.
We can merge this PR first, and I will following up with another one after the test to add the fix.

emilyhcliu · 2023-11-15T19:42:38Z

I think the atms yaml for bufr2ioda is missing the sensor in the following section:

          sensorScanAngle:
            sensorScanAngle:
              fieldOfViewNumber: "*/FOVN"
              scanStart: -52.725
              scanStep: 1.110
              sensor: atms

CoryMartin-NOAA · 2023-11-15T19:43:26Z

@emilyhcliu agreed, now I'm getting a splits issue, which is related to my script, so I will still need to do a bit more debugging. Standby.

CoryMartin-NOAA · 2023-11-15T19:51:39Z

The latest commit works:

/work2/noaa/da/cmartin/gdas-validation/comrot/gdas_eval_satwind_JEDI/gdas.20210801/00/obs/gdas.t00z.atms.n20.tm00.nc
/work2/noaa/da/cmartin/gdas-validation/comrot/gdas_eval_satwind_JEDI/gdas.20210801/00/obs/gdas.t00z.atms.npp.tm00.nc

But @RussTreadon-NOAA is right, 10 mins is no longer sufficient. We need to parallelize this. I will look into that next.

emilyhcliu · 2023-11-15T19:52:18Z

@emilyhcliu agreed, now I'm getting a splits issue, which is related to my script, so I will still need to do a bit more debugging. Standby.

Here is the updated ATMS YAML for bufr2ioda:
/work/noaa/da/eliu/JEDI-iodaconv/run_atms/bufr_ncep_atms_remap.yaml

I tested it using a stand-alone IODA-bundle. It worked.

You can grab this one and add it to the GDASApp. Please feel free to rename the yaml.

RussTreadon-NOAA

Fold feature/gdas-validation-driver at 5a8a535 into working copy of gdas-validation. Run 2021080100 gdasprepatmiodaobs. Job ran to completion with rc=0.

Approve.

CoryMartin-NOAA added 3 commits November 15, 2023 09:26

Save commit

898fb55

debugging

d7e9ec8

working version I think

3b171d7

CoryMartin-NOAA requested review from RussTreadon-NOAA and emilyhcliu November 15, 2023 17:26

CoryMartin-NOAA self-assigned this Nov 15, 2023

coding norms

eb0ad33

RussTreadon-NOAA reviewed Nov 15, 2023

View reviewed changes

This works

62e2f10

CoryMartin-NOAA requested a review from RussTreadon-NOAA November 15, 2023 19:52

Remove height of station, add N21

5a8a535

RussTreadon-NOAA approved these changes Nov 15, 2023

View reviewed changes

CoryMartin-NOAA merged commit 5c305aa into feature/gdas-validation Nov 15, 2023

CoryMartin-NOAA deleted the feature/gdas-validation-driver branch November 15, 2023 20:08

CoryMartin-NOAA mentioned this pull request Nov 15, 2023

Generalize the BUFR to IODA driver script #728

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emilyhcliu commented Nov 15, 2023 •

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