Add run and finalize methods to marine LETKF task #2944

AndrewEichmann-NOAA · 2024-09-19T19:03:30Z

Description

Adds run and finalize methods to marine LETKF task, experiment yaml for gw-ci in GDASApp, workflow additions, removes bugs found on the way, and completes the bulk of the work on LETKF task. Conversion of fields to increments pending.

Partially resolves NOAA-EMC/GDASApp#1091 and NOAA-EMC/GDASApp#1251

Mutual dependency with GDASApp PR NOAA-EMC/GDASApp#1287 and IC fix file issue #2944 (comment)

Type of change

Bug fix (fixes something broken)
New feature (adds functionality)
Maintenance (code refactor, clean-up, new CI test, etc.)

Change characteristics

Is this a breaking change (a change in existing functionality)? NO
Does this change require a documentation update? NO
Does this change require an update to any of the following submodules? YES (If YES, please add a link to any PRs that are pending.)
- EMC verif-global
- GDAS
- GFS-utils
- GSI
- GSI-monitor
- GSI-utils
- UFS-utils
- UFS-weather-model
- wxflow

How has this been tested?

Example:

Cycled test on Hera

Checklist

Any dependent changes have been merged and published
My code follows the style guidelines of this project
I have performed a self-review of my own code
I have commented my code, particularly in hard-to-understand areas
My changes generate no new warnings
New and existing tests pass with my changes
I have made corresponding changes to the documentation if necessary

AndrewEichmann-NOAA · 2024-09-19T19:04:06Z

FYI @guillaumevernieres @CatherineThomas-NOAA

ush/python/pygfs/task/marine_letkf.py

guillaumevernieres

We'll probably have to rearrange things between your PR and mine at some point, but this looks good to me. Thanks for doing this @AndrewEichmann-NOAA .

guillaumevernieres · 2024-09-19T20:06:31Z

ush/python/pygfs/task/marine_letkf.py

+ exec_cmd_gridgen.add_default_arg(self.task_config.GRIDGEN_EXEC)
+ exec_cmd_gridgen.add_default_arg(self.task_config.GRIDGEN_YAML)
+
+ try:


I know this will be refactored soon, but maybe use this in the meantime marine_da_utils.py#L18 ?

Add an issue and maybe also a TODO if you don't want to address this in this PR. This will be refactored when we start making use of the Jedi class.

changed - I forgot about this comment

workflow/rocoto/gfs_tasks.py

jobs/JGLOBAL_MARINE_BMAT

WalterKolczynski-NOAA · 2024-09-27T04:34:13Z

parm/config/gfs/config.com

@@ -82,12 +82,14 @@ declare -rx COM_OCEAN_HISTORY_TMPL=${COM_BASE}'/model/ocean/history'
 declare -rx COM_OCEAN_RESTART_TMPL=${COM_BASE}'/model/ocean/restart'
 declare -rx COM_OCEAN_INPUT_TMPL=${COM_BASE}'/model/ocean/input'
 declare -rx COM_OCEAN_ANALYSIS_TMPL=${COM_BASE}'/analysis/ocean'
+declare -rx COM_OCEAN_LETKF_TMPL=${COM_BASE}'/analysis/ocean/letkf'


What files get written to the letkf directories vs the regular component analysis directories?

These are the analysis files from the LETKF, which are separate from the variational analysis files

ush/python/pygfs/task/marine_letkf.py

workflow/rocoto/gfs_tasks.py

aerorahul · 2024-10-11T13:53:36Z

env/WCOSS2.env

- export NTHREADS_MARINEANALLETKF=${NTHREADSmax}
- export APRUN_MARINEANALLETKF="${APRUN_default} --cpus-per-task=${NTHREADS_MARINEANALLETKF}"
+ export NTHREADS_MARINEANLLETKF=${NTHREADSmax}
+ export APRUN_MARINEANLLETKF="${APRUN_default} --cpus-per-task=${NTHREADS_MARINEANLLETKF}"


This is incorrect specification for WCOSS2.

@aerorahul Is there an example you could suggest to work off of? There seem to be a number of choices.

Since JEDI does not yet employ threads, this could simply be:

export APRUN_MARINEANLLETKF="${APRUN_default}"

When threading do come into play,

export APRUN_MARINEANLLETKF="${APRUN_default} --ppn ${tasks_per_node}--cpu-bind depth --depth=${NTHREADS_MARINEANLLETKF}"

You could see the JEDI atm sections of this code for reference.

ush/forecast_postdet.sh

aerorahul

some minor comments.
approved pending tests passing.

WalterKolczynski-NOAA

A couple very minor things.

workflow/rocoto/gfs_tasks.py

jobs/JGLOBAL_MARINE_ANALYSIS_LETKF

WalterKolczynski-NOAA · 2024-10-15T19:23:34Z

Also need to resolve pynorms failures.

Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

WalterKolczynski-NOAA · 2024-10-17T03:04:01Z

@AndrewEichmann-NOAA pynorms is still failing:

checking ./ush/python/pygfs/task/marine_letkf.py
./ush/python/pygfs/task/marine_letkf.py:46:8: E114 indentation is not a multiple of 4 (comment)
./ush/python/pygfs/task/marine_letkf.py:55:78: W291 trailing whitespace
./ush/python/pygfs/task/marine_letkf.py:57:1: W293 blank line contains whitespace

https://github.com/NOAA-EMC/global-workflow/actions/runs/11376852041/job/31650003088?pr=2944

guillaumevernieres

Seem inline comments

guillaumevernieres · 2024-10-17T15:49:50Z

ci/cases/pr/C48mx500_hybAOWCDA.yaml

+skip_ci_on_hosts:
+ - wcoss2
+ - orion
+ - hercules


This test needs to be turned off on all machines for now. The GDASApp subset of test might work, but the full gw-ci test won't.

gaea and hera added

env/HERA.env

guillaumevernieres · 2024-10-17T16:02:04Z

ush/python/pygfs/task/marine_letkf.py

+ exec_cmd_gridgen.add_default_arg(self.task_config.GRIDGEN_EXEC)
+ exec_cmd_gridgen.add_default_arg(self.task_config.GRIDGEN_YAML)
+
+ try:


Add an issue and maybe also a TODO if you don't want to address this in this PR. This will be refactored when we start making use of the Jedi class.

workflow/rocoto/gfs_tasks.py

jobs/JGLOBAL_MARINE_ANALYSIS_LETKF

aerorahul · 2024-10-17T19:51:52Z

jobs/JGLOBAL_MARINE_ANALYSIS_LETKF

@@ -11,12 +18,19 @@ GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")

 gPDY=${GDATE:0:8}
 gcyc=${GDATE:8:2}
+export GDUMP="gdas"
+export GDUMP_ENS="enkf${GDUMP}"
+export RUN="${GDUMP}"


@WalterKolczynski-NOAA I don't think RUN can be assigned here. It is set at the rocoto level, correct?

changeed to walter' suggestion

Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

AndrewEichmann-NOAA added 14 commits August 21, 2024 18:01

debugging for ocean ensemble run

20e48a1

Merge branch 'develop' into feature/ens-WCDA-ctest

16d805f

fix ci stager for ensemble + DO_IAU

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Merge branch 'develop' into feature/ens-WCDA-ctest

9501e74

removing ice var changer

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Merge branch 'develop' into feature/ens-WCDA-ctest

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the latests

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Merge branch 'develop' into feature/ens-WCDA-ctest

0dcf183

removal of cruft

6a2cd3d

undo odd thing

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style

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style

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style

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removed personal bits

1e53cb5

AndrewEichmann-NOAA mentioned this pull request Sep 19, 2024

Completes LETKF task, adds WCDA CI test NOAA-EMC/GDASApp#1287

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Add enkfgdas.20210324 to ICSDIR/C48mx500 #2945

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AndrewEichmann-NOAA and others added 6 commits September 20, 2024 09:24

Merge branch 'develop' into feature/ens-WCDA-ctest

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the great deawkwarding

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using communal ICs

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Merge branch 'develop' into feature/ens-WCDA-ctest

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renaming

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rearrange task deps

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AndrewEichmann-NOAA commented Sep 26, 2024

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Merge branch 'develop' into feature/ens-WCDA-ctest

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AndrewEichmann-NOAA added 2 commits September 30, 2024 13:42

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AndrewEichmann-NOAA added 2 commits October 10, 2024 14:42

Merge branch 'develop' into feature/ens-WCDA-ctest

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using GDUMP_ENS

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AndrewEichmann-NOAA added 2 commits October 16, 2024 17:50

Merge branch 'develop' into feature/ens-WCDA-ctest

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add underscore in task names

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AndrewEichmann-NOAA dismissed aerorahul’s stale review via 8024e5f October 16, 2024 18:20

AndrewEichmann-NOAA and others added 3 commits October 16, 2024 18:23

comment pruning

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Update workflow/rocoto/gfs_tasks.py

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Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

review stuff

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AndrewEichmann-NOAA requested review from aerorahul and WalterKolczynski-NOAA October 17, 2024 01:48

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AndrewEichmann-NOAA requested review from KateFriedman-NOAA, DavidHuber-NOAA and TerrenceMcGuinness-NOAA as code owners October 18, 2024 14:55

Update jobs/JGLOBAL_MARINE_ANALYSIS_LETKF

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Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

AndrewEichmann-NOAA requested review from aerorahul, WalterKolczynski-NOAA and guillaumevernieres October 18, 2024 17:38

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Add run and finalize methods to marine LETKF task #2944

Add run and finalize methods to marine LETKF task #2944

AndrewEichmann-NOAA commented Sep 19, 2024 •

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Add run and finalize methods to marine LETKF task #2944

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Add run and finalize methods to marine LETKF task #2944

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AndrewEichmann-NOAA commented Sep 19, 2024 • edited Loading

Description

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How has this been tested?

Checklist

AndrewEichmann-NOAA commented Sep 19, 2024

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AndrewEichmann-NOAA commented Sep 19, 2024 •

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