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Copy land increments and land DA confs to COM #1797

Merged
merged 13 commits into from
Aug 23, 2023
Merged

Copy land increments and land DA confs to COM #1797

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bdd67fc
Shift window_begin 1 second backward
jiaruidong2017 Aug 12, 2023
5dd9539
Fix python norm issue
jiaruidong2017 Aug 12, 2023
d38d227
Add 1S to the wind lenght and remove a space.
jiaruidong2017 Aug 15, 2023
0060e35
Set the window lenght 6 hours + 2 seconds to make DA window
jiaruidong2017 Aug 15, 2023
a56a834
Change the window length.
jiaruidong2017 Aug 15, 2023
69f1d67
Merge branch 'develop' into feature/window_shift
jiaruidong2017 Aug 15, 2023
35104d9
Update GDASApp commit hash.
jiaruidong2017 Aug 16, 2023
81cd817
Update the window length to 6 hr 1 sec.
jiaruidong2017 Aug 16, 2023
a5e36be
Merge branch 'develop' into feature/window_shift
jiaruidong2017 Aug 18, 2023
4e22b5a
create a COM_CONF_TMPL and copy YAML file into COM_CONF.
jiaruidong2017 Aug 18, 2023
696fbf1
Address the reviewer comments.
jiaruidong2017 Aug 18, 2023
c32b1b4
Revert the changes for window manipulation.
jiaruidong2017 Aug 23, 2023
7c4b99c
Merge branch 'develop' into feature/window_shift
jiaruidong2017 Aug 23, 2023
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2 changes: 1 addition & 1 deletion Externals.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ protocol = git
required = False

[GDASApp]
hash = 09757ce
hash = 2774a10
local_path = sorc/gdas.cd
repo_url = https://github.com/NOAA-EMC/GDASApp.git
protocol = git
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2 changes: 1 addition & 1 deletion sorc/checkout.sh
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Expand Up @@ -160,7 +160,7 @@ if [[ ${checkout_gsi} == "YES" ]]; then
fi

if [[ ${checkout_gdas} == "YES" ]]; then
checkout "gdas.cd" "https://github.com/NOAA-EMC/GDASApp.git" "09757ce"; errs=$((errs + $?))
checkout "gdas.cd" "https://github.com/NOAA-EMC/GDASApp.git" "2774a10"; errs=$((errs + $?))
fi

if [[ ${checkout_gsi} == "YES" || ${checkout_gdas} == "YES" ]]; then
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28 changes: 25 additions & 3 deletions ush/python/pygfs/task/land_analysis.py
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Expand Up @@ -34,6 +34,7 @@ def __init__(self, config):

_res = int(self.config['CASE'][1:])
_window_begin = add_to_datetime(self.runtime_config.current_cycle, -to_timedelta(f"{self.config['assim_freq']}H") / 2)
_window_begin = add_to_datetime(_window_begin, -to_timedelta(f"1S"))
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to do this "correctly, now don't we need to make the window_length 6hours + 1 second?

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@CoryMartin-NOAA I conducted and compared two runs: one with window length 6 hours and the other with 6 hours + 1 second. They do show some difference from the land increment files as below:

Tile 1: 
Variable Group Count        Sum     AbsSum          Min        Max       Range        Mean      StdDev
snodl    /       432 0.00534215 0.00534219 -4.60635e-09 0.00056797 0.000567975 1.23661e-05 6.58902e-05

Tile 2: 
Variable Group Count       Sum  AbsSum      Min     Max   Range         Mean   StdDev
snodl    /      1213 -0.570553 65.0728 -3.67096 3.36201 7.03297 -0.000470365 0.306991

Tile 3: 
Variable Group Count Sum AbsSum     Min     Max   Range Mean StdDev
snodl    /       982 nan    nan -94.825 98.1387 192.964  nan    nan
vtype    /       105 nan    nan     inf    -inf    -inf  nan    nan
slmsk    /       105 nan    nan     inf    -inf    -inf  nan    nan

Tile 4, 5, 6 are identical.

Let's talk at tomorrow's meeting.

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@CoryMartin-NOAA @barlage When I conducted the snow DA cycling run with window length 6 hours + 2 seconds which make the DA window centering at the cycle time, all the nan values were gone. Therefore, the DA window centering at the cycle time is important.

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CORRECTIONS:

My above statements are incorrect, because there are still nan values when the above setting with the DA window beginning at 1 second back and window length 6 hours + 2 seconds.

The above with no nan values came from the experiment with the DA window beginning at 2 second back and window length 6 hours + 1 seconds.

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@barlage barlage Aug 15, 2023 •
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Since @CoryMartin-NOAA questioned in the meeting earlier, we looked at an increment file and not all of the grids are NaN, only about 100-200 and they look to be in locations where there are snow observations, which can seen from the above nccmp. Also, there must be some increment limits in the add_increment code since these do not affect the analysis.

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@CoryMartin-NOAA Okay, I will change the window length to 6hr 1sec.

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@aerorahul aerorahul Aug 16, 2023 •
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I don't understand, if the results are the same for 6hr, 6hr-1s, 6hr+1s, then why make the change?
Also, shouldn't this be handled in the observation processing part rather than in the workflow?
Consider the case where the observations are in a single file for 24h (for e.g.), shouldn't this be teased out in the yaml?

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@aerorahul this is because the 'JEDI' window convention is the opposite of the 'NCEP' window convention, and we lost that battle with Yannick a while ago. While it may be identical in this case, it shouldn't be. Observations at exactly 03z would not make it into the 06z analysis without this change. I don't quite understand you comment in the second sentence, this is what defines the window variable that goes into the templated YAML.

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@aerorahul aerorahul Aug 16, 2023 •
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I understand. Lets discuss offline.

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Thanks @CoryMartin-NOAA for the detailed explanations.
@aerorahul Without this change, about several hundreds of observations will be lost in each cycle. For example, the observations increased from 1718 to 2161 with this changes.

_letkfoi_yaml = os.path.join(self.runtime_config.DATA, f"{self.runtime_config.RUN}.t{self.runtime_config['cyc']:02d}z.letkfoi.yaml")

# Create a local dictionary that is repeatedly used across this class
Expand All @@ -44,7 +45,7 @@ def __init__(self, config):
'npz_ges': self.config.LEVS - 1,
'npz': self.config.LEVS - 1,
'LAND_WINDOW_BEGIN': _window_begin,
'LAND_WINDOW_LENGTH': f"PT{self.config['assim_freq']}H",
'LAND_WINDOW_LENGTH': f"PT{self.config['assim_freq']}H1S",
'OPREFIX': f"{self.runtime_config.RUN}.t{self.runtime_config.cyc:02d}z.",
'APREFIX': f"{self.runtime_config.RUN}.t{self.runtime_config.cyc:02d}z.",
'jedi_yaml': _letkfoi_yaml
Expand Down Expand Up @@ -323,8 +324,10 @@ def execute(self) -> None:
def finalize(self) -> None:
"""Performs closing actions of the Land analysis task
This method:
- copies analysis back to COM/ from DATA/
- tar and gzips the JEDI diagnostic files
- tar and gzip the output diag files and place in COM/
- copy the generated YAML file from initialize to the COM/
- copy the analysis files to the COM/
- copy the increment files to the COM/

Parameters
----------
Expand All @@ -336,6 +339,15 @@ def finalize(self) -> None:
statfile = os.path.join(self.task_config.COM_LAND_ANALYSIS, f"{self.task_config.APREFIX}landstat.tgz")
self.tgz_diags(statfile, self.task_config.DATA)

logger.info("Copy full YAML to COM")
src = os.path.join(self.task_config['DATA'], f"{self.task_config['CDUMP']}.t{self.runtime_config['cyc']:02d}z.letkfoi.yaml")
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Suggested change
src = os.path.join(self.task_config['DATA'], f"{self.task_config['CDUMP']}.t{self.runtime_config['cyc']:02d}z.letkfoi.yaml")
src = os.path.join(self.task_config['DATA'], f"{self.task_config['RUN']}.t{self.runtime_config['cyc']:02d}z.letkfoi.yaml")

Please don't use CDUMP anymore.

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Also, isn't this already defined as self.task_config.APREFIX? Why do we need to reconstruct that again here?

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Thanks @aerorahul for quick review. Good catch, and I made the changes as suggested.

dest = os.path.join(self.task_config.COM_LAND_ANALYSIS, f"{self.task_config['CDUMP']}.t{self.runtime_config['cyc']:02d}z.letkfoi.yaml")
yaml_copy = {
'mkdir': [self.task_config.COM_LAND_ANALYSIS],
'copy': [[src, dest]]
}
FileHandler(yaml_copy).sync()
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Why?
COM is for data not configuration. The UFS-weather-model has set a precedent for copying namelists and configuration stuff into COM. If there is a need to copy this data for every cycle, we need a proper solution with a well defined set of requirements.

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Why not? This is a few kb file that is a record of the exact configuration needed to reproduce results. Especially in the land case, this is different at 18z than it is at other cycles. When observations and QC have to be turned on/off these YAMLs will not always be identical and should be retained.

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Thanks @CoryMartin-NOAA. In addition, I include copying the YAML files for archive to keep consistent with other DA component such as aero DA.

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@aerorahul aerorahul Aug 17, 2023 •
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An update to this comment:

After discussions w/ NCO, if we wish to retain cycle specific configuration artifacts such as namelists, etc. that are not already part of HOMEgfs, we can do so in a single location in COM. @CoryMartin-NOAA and @aerorahul discussed a good place for said configuration artifacts would be ROTDIR/RUN.PDY/cyc/conf.
The jobs will need to ensure that they identify the artifacts uniquely; for e.g. input.nml from the ufs-weather-model should be saved as ufs_input.nml

This will require creating a COM_CONF_TMPL in config.com and then filling the template with appropriate substitutions in the j-jobs that wish to save the artifacts.

Please let me know if you have any questions.
@WalterKolczynski-NOAA FYI

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Thanks @aerorahul for the updates.
@CoryMartin-NOAA @aerorahul Do you want me to include this change in this PR by putting the yaml file into the ROTDIR/RUN.PDY/cyc/conf?

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As suggested, I create COM_CONF_TMPL in config.com and copy the YAML file into ROTDIR/RUN.PDY/cyc/conf. I still keep using the previous name (e.g., gdas.t18z.letkfoi.yaml). What do you suggest the change for the file name?


logger.info("Copy analysis to COM")
template = f'{to_fv3time(self.task_config.current_cycle)}.sfc_data.tile{{tilenum}}.nc'
anllist = []
Expand All @@ -346,6 +358,16 @@ def finalize(self) -> None:
anllist.append([src, dest])
FileHandler({'copy': anllist}).sync()

logger.info('Copy increments to COM')
template = f'landinc.{to_fv3time(self.task_config.current_cycle)}.sfc_data.tile{{tilenum}}.nc'
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inclist = []
for itile in range(1, self.task_config.ntiles + 1):
filename = template.format(tilenum=itile)
src = os.path.join(self.task_config.DATA, 'anl', filename)
dest = os.path.join(self.task_config.COM_LAND_ANALYSIS, filename)
inclist.append([src, dest])
FileHandler({'copy': inclist}).sync()

@staticmethod
@logit(logger)
def get_bkg_dict(config: Dict) -> Dict[str, List[str]]:
Expand Down