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Restore dry deposition output in GCHP & GCClassic fullchem benchmark simulations #2144

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merged 3 commits into from
Aug 28, 2024

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yantosca
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@yantosca yantosca commented Feb 2, 2024

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Name: Bob Yantosca
Institution: Harvard + GCST

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Describe the update

This is the companion PR to #2139. We have updated the template HISTORY.rc.fullchem files for both GCHP and GCClassic so as to activate the DryDep collection in benchmark simulations. Also, for the GCHP simulation, we have reduced the number of species output to netCDF to only those that are absolutely needed for the benchmarks (as described in #2135).

Expected changes

This PR will activate dry deposition output for full-chemistry benchmark simulations, so that plots of dry deposition velocity can be made. Also the dry-deposition flux of O3 will be archived so as to be able to compute the Ox budget.

Related Github Issue(s)

@yantosca yantosca self-assigned this Feb 2, 2024
@yantosca yantosca added category: Feature Request New feature or request topic: Diagnostics Related to output diagnostic data topic: Benchmarking and Testing Related to CI, integration tests, or scientific benchmarking labels Feb 2, 2024
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yantosca commented Feb 2, 2024

I left the base branch as main so that this PR wouldn't auto-close when dev/14.3.0 was removed. This can go into the dev/14.4.0 branch once we start working on it.

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lizziel commented Feb 6, 2024

Do we need to turn on dry deposition diagnostics for GCHP and GC-Classic fullchem benchmarks by default? I think the dry dep diagnostics are only needed for 1-year benchmarks.

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That's correct, I think. The setup script I have for GCClassic 1-year benchmark uncomments the DryDep (and other) diagnostics in HISTORY.rc. We could set up a similar script for GCHP.

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Alternatively, we could activate the drydep plots (for a subset of species) in 1-month benchmarks. It might be useful to diagnose changes there as well. @yantosca any thoughts?

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yantosca commented Feb 6, 2024

Yes, I was thinking we could activate a subset of species for the 1-month as well. That way we can detect any changes caused by LAI updates etc.

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This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the Stale bot from closing this issue.

@stale stale bot added the stale No recent activity on this issue label Apr 22, 2024
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@yantosca What is the status of this PR? Should it be included in 14.4.0?

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@msulprizio: It could go into 14.4.0. We'd need to doublecheck the HISTORY.rc files and maybe also make a corresponding update in the GCPy template YAML files though. I haven't had time to work on this lately but we could try to get it in before the 14.4.0 freeze date.

@stale stale bot removed the stale No recent activity on this issue label Apr 22, 2024
@lizziel lizziel changed the base branch from main to dev/14.4.0 April 22, 2024 15:35
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lizziel commented Apr 22, 2024

It looks like integration tests should be able to test out the HISTORY.rc file changes, and the GCPy updates could go in later, whenever we decide to add drydep plots to the benchmark. I updated the milestone to be 14.4.0.

@yantosca yantosca deleted the branch dev/14.5.0 May 30, 2024 18:55
@yantosca yantosca closed this May 30, 2024
@msulprizio msulprizio reopened this May 30, 2024
@msulprizio msulprizio changed the base branch from dev/14.4.0 to main May 30, 2024 19:17
@yantosca yantosca changed the base branch from main to dev/14.5.0 August 6, 2024 19:46
run/GCClassic/HISTORY.rc.templates/HISTORY.rc.fullchem
- Change ##'DryDep' -> #'DryDep', which will activate this collection
  in benchmark simulations.

run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem
- Change @#'DryDep' -> #'DryDep', which will activate this collection
  in benchmark simulations.
- Also reduce the DryDep collection species to only those species
  we need for benchmark plots/tables

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca yantosca force-pushed the feature/restore-drydep-in-bmk branch from a3f58bc to cb86824 Compare August 6, 2024 20:10
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yantosca commented Aug 6, 2024

I have rebased this PR off 14.5.0-alpha.4 and will rerun integration tests.

@yantosca yantosca added this to the 14.5.0 milestone Aug 6, 2024
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yantosca commented Aug 6, 2024

All GEOS-Chem Classic integration tests passed:

==============================================================================
GEOS-Chem Classic: Execution Test Results

GCClassic #0c22a3a GEOS-Chem submod update: PR #2352 post-merge fix (rebuild KPP files)
GEOS-Chem #cb86824f5 Archive "Drydep" diags in fullchem bmks; Reduce GCHP "DryDep" output
HEMCO     #e68ebae HEMCO 3.9.2 release

Using 24 OpenMP threads
Number of execution tests: 28

Submitted as SLURM job: 42911370
==============================================================================

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The DryDep collection files were generated in the fullchem_benchmark run directory:

$ gc_4x5_merra2_fullchem_benchmark/OutputDir
$ ls
GEOSChem.AdvFluxVert.20190701_0000z.nc4  GEOSChem.Metrics.20190701_0000z.nc4
GEOSChem.AerosolMass.20190701_0000z.nc4  GEOSChem.SpeciesConc.20190701_0000z.nc4
GEOSChem.Aerosols.20190701_0000z.nc4     geoschem_species_metadata.yml
GEOSChem.DryDep.20190701_0000z.nc4       GEOSChem.StateMet.20190701_0000z.nc4
GEOSChem.JValues.20190701_0000z.nc4      HEMCO_diagnostics.201907010000.nc

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yantosca commented Aug 6, 2024

All GCHP integration tests passed:

==============================================================================
GCHP: Execution Test Results

GCHP      #548c753 GEOS-Chem submod update: PR #2352 post-merge fix (rebuild KPP files)
GEOS-Chem #cb86824f5 Archive "Drydep" diags in fullchem bmks; Reduce GCHP "DryDep" output
HEMCO     #

Number of execution tests: 11

Submitted as SLURM job: 42912361
==============================================================================
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Also, the "DryDep" collection file was created in the gchp_merra2_fullchem_benchmark run directory:

$ cd rundirs/gchp_merra2_fullchem_benchmark/OutputDir/
$ ls
GEOSChem.AerosolMass.20190701_0000z.nc4          GEOSChem.GCHPctmEnvLevEdge.20190701_0000z.nc4
GEOSChem.Aerosols.20190701_0000z.nc4             GEOSChem.JValues.20190701_0000z.nc4
GEOSChem.DryDep.20190701_0000z.nc4               GEOSChem.Metrics.20190701_0000z.nc4
GEOSChem.Emissions.20190701_0000z.nc4            GEOSChem.SpeciesConc.20190701_0000z.nc4
GEOSChem.FV3Dynamics.20190701_0000z.nc4          geoschem_species_metadata.yml
GEOSChem.GCHPctmEnvLevCenter.20190701_0000z.nc4  GEOSChem.StateMet.20190701_0000z.nc4

@yantosca yantosca marked this pull request as ready for review August 6, 2024 22:03
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Thanks @yantosca. Please see my comments below.

CHANGELOG.md Show resolved Hide resolved
run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem Outdated Show resolved Hide resolved
CHANGELOG.md
- Restored missing line that was inadvertenly deleted
- Place `` around "State_Chm%CH4_EMIS"

run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem
- Removed extra slash in comments

Signed-off-by: Bob Yantosca <[email protected]>
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Now approved for merging. Thanks @yantosca!

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yantosca commented Aug 7, 2024

Thanks @msulprizio. I am waiting on the results of a 1-month benchmark. I will merge up into 14.5.0 (locally) and rerun integration tests just to make sure there aren't any merge issues.

run/GCHP/HISTORY.rc.fullchem
- Add the DryDepChm_O3 and DryDepMix_O3 fields to the DryDep colletction
  out-of-bounds error.  This is to be consistent w/ GCClassic as well.

Signed-off-by: Bob Yantosca <[email protected]>
yantosca added a commit that referenced this pull request Aug 20, 2024
run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem
- Only keep the fields that are necessary for fullchem benchmarks
  in the DryDep collection.  This is similar to what is being done
  in PR #2144 (which will be merged later).

Signed-off-by: Bob Yantosca <[email protected]>
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After merging (locally) atop PR #2318, all GEOS-Chem Classic integration tests passed, except ModelE2.1.

==============================================================================
GEOS-Chem Classic: Execution Test Results

CodeDir   : edaa239 GEOS-Chem & HEMCO updates: Merge PR #2318, PR #284, PR #285
GEOS-Chem : c7332ed7a Merge PR #2144 (Restore drydep output in fullchem benchmarks)
HEMCO     : d0d5fca PR #285 post-merge fix: Update CHANGELOG.md
Cloud-J   : d20050f Update version to 7.7.3
HETP      : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Using 24 OpenMP threads
Number of execution tests: 30

Submitted as SLURM job: 44355766
==============================================================================
...
gc_2x25_ModelE2.1_fullchem..........................Execute Simulation....FAIL
... 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 29
Execution tests failed: 1
Execution tests not yet completed: 0

The failure is caused by a missing data file on the GCAP2 40L grid, as described in PR #2427.

@yantosca yantosca merged commit c7332ed into dev/14.5.0 Aug 28, 2024
@yantosca yantosca deleted the feature/restore-drydep-in-bmk branch August 28, 2024 15:07
yantosca added a commit to geoschem/gcpy that referenced this pull request Aug 29, 2024
… bmks)

This merge brings PR # (Add the DryDep collection to the benchmark summary
table, and DryDepVel plots to 1-mon cloud benchmarks, by @yantosca) into
the GCPy development stream.

The GEOS-Chem `DryDep` collection was restored to all fullchem benchmark
simulations in geoschem/geos-chem#2144.  This is
the corresponding GCPy PR, which includes code to:
1. Add the `DryDep` collection to the benchmark summary table
2. Plot dry deposition velocities in 1-hr cloud benchmarks

Signed-off-by: Bob Yantosca <[email protected]>
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