Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add sanity check for missing molecular weights; add missing MW for HgBrO #1843

Merged
merged 3 commits into from Jul 6, 2023
Merged

Add sanity check for missing molecular weights; add missing MW for HgBrO #1843

merged 3 commits into from Jul 6, 2023

Conversation

yantosca
Copy link
Contributor

Name and Institution (Required)

Name: Bob Yantosca
Institution: Harvard + GCST

Confirm you have reviewed the following documentation

Describe the update

This PR corrects an issue first described in #1832 by @mvermeuel:

The issue was that I was not defining a dummy species to track the loss rate of H2O2 (LH2O2) in my species_database.yml file but I was in my restart file. The program gave LH2O2 a molecular weight of -9999 which then gave an error when trying to take the square root.

To prevent errors such as these, we now throw an error if the molecular weight is undefined. We have added an error trap in Headers/species_database_mod.F90 in the "sanity checks" section.

Expected changes

If a molecular weight is missing in the species database, you will get an error such as:

===============================================================================
GEOS-Chem ERROR: MW_g for species NO3 is undefined!
 -> at Init_Species_Database (in module Headers/species_database_mod.F90
===============================================================================

===============================================================================
GEOS-Chem ERROR: Error encountered in routine "Init_Species_Database"!
 -> at Init_State_Chm (in module Headers/state_chm_mod.F90)
===============================================================================

===============================================================================
GEOS-Chem ERROR: Error encountered within call to "Init_State_Chm"!
 -> at GC_Init_StateObj (in GeosCore/gc_environment_mod.F90)
===============================================================================

===============================================================================
GEOS-CHEM ERROR: Error encountered in "GC_Init_StateObj!"!
STOP at  -> at GEOS-Chem (in GeosCore/main.F90)
===============================================================================

Otherwise this will not change any results.

Reference(s)

N/A

Related Github Issue(s)

Closes #1832

@yantosca
Add error trap for missing molecular weights
6f1e7b9 
Headers/species_database_mod.F90
- Add a sanity check to make sure that the MW_g (molecular weight)
  field of each species is defined to a valid value.  If the MW_g
  is undefined (i.e. contains the value MISSING_REAL), then stop
  with an error.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca yantosca added category: Feature Request New feature or request topic: Structural Modifications Related to GEOS-Chem structural modifications (as opposed to scientific updates) no-diff-to-benchmark This update will not change the results of fullchem benchmark simulations labels Jun 21, 2023
@yantosca yantosca requested a review from msulprizio June 21, 2023 19:21
@yantosca yantosca self-assigned this Jun 21, 2023
@yantosca yantosca changed the title Add sanity check for missing molecular weights Add sanity check for missing molecular weights; add missing MW for HgBrO Jun 27, 2023
@yantosca
Bug fix: Use mol wt of atomic Hg for HgBr0 in Hg simulation
8dea9d5 
run/shared/species_database_hg.yml
- Add missing molecular weight for HgBrO.  Use 200.59 g/mol which is
  the mol wt of atomic Hg.  This is used for the other Hg compounds
  as well.  Add comments stating such.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca
Copy link
Contributor Author

In commit 8dea9d5, the following fixes were made:

  1. Add missing MW of 200.59 for species HgBrO in run/shared/species_database.yml
  2. Add comments denoting that Hg species carry the MW of atomic Hg in run/shared/species_database.yml
  3. Updated CHANGELOG.md accordingly.

Integration tests are being re-run. The missing MW for HgBrO caused the Hg execution test to fail.

@yantosca yantosca changed the base branch from main to dev/14.2.1 June 28, 2023 15:23
@yantosca
Copy link
Contributor Author

All GEOS-Chem Classic integration tests passed, except for TOMAS. The TOMAS failures are due to the issue reported in #1841.

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

GCClassic #ae031f8 GEOS-Chem and HEMCO submodule updates: Update transport tracer simulation for consistency with GMAO's tracer gridded component
GEOS-Chem #0f3097d2c Merge PR #1846 (branch 'feature/add_geosit_as_met_option') into dev/14.2.0
HEMCO     #6e2a808 Merge PR #214 (branch 'feature/update-transport-tracers') into dev/3.7.0

Using 24 OpenMP threads
Number of execution tests: 26

Submitted as SLURM job: 59884221
==============================================================================
 
Execution tests:
------------------------------------------------------------------------------
gc_05x0625_NA_47L_merra2_CH4........................Execute Simulation....PASS
gc_05x0625_NA_47L_merra2_fullchem...................Execute Simulation....PASS
gc_4x5_47L_merra2_fullchem..........................Execute Simulation....PASS
gc_4x5_47L_merra2_fullchem_TOMAS15..................Execute Simulation....FAIL
gc_4x5_47L_merra2_fullchem_TOMAS40..................Execute Simulation....FAIL
gc_4x5_merra2_aerosol...............................Execute Simulation....PASS
gc_4x5_merra2_carbon................................Execute Simulation....PASS
gc_4x5_merra2_CH4...................................Execute Simulation....PASS
gc_4x5_merra2_CO2...................................Execute Simulation....PASS
gc_4x5_merra2_fullchem..............................Execute Simulation....PASS
gc_4x5_merra2_fullchem_aciduptake...................Execute Simulation....PASS
gc_4x5_merra2_fullchem_APM..........................Execute Simulation....PASS
gc_4x5_merra2_fullchem_benchmark....................Execute Simulation....PASS
gc_4x5_merra2_fullchem_complexSOA...................Execute Simulation....PASS
gc_4x5_merra2_fullchem_complexSOA_SVPOA.............Execute Simulation....PASS
gc_4x5_merra2_fullchem_LuoWd........................Execute Simulation....PASS
gc_4x5_merra2_fullchem_marinePOA....................Execute Simulation....PASS
gc_4x5_merra2_fullchem_RRTMG........................Execute Simulation....PASS
gc_4x5_merra2_Hg....................................Execute Simulation....PASS
gc_4x5_merra2_metals................................Execute Simulation....PASS
gc_4x5_merra2_POPs_BaP..............................Execute Simulation....PASS
gc_4x5_merra2_tagCH4................................Execute Simulation....PASS
gc_4x5_merra2_tagCO.................................Execute Simulation....PASS
gc_4x5_merra2_tagO3.................................Execute Simulation....PASS
gc_4x5_merra2_TransportTracers......................Execute Simulation....PASS
gc_4x5_merra2_TransportTracers_LuoWd................Execute Simulation....PASS
 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 24
Execution tests failed: 2
Execution tests not yet completed: 0

@yantosca
Copy link
Contributor Author

All GCHP integration tests (except for TransportTracers) passed. The TransportTracers issue is fixed in PR #1840.

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

GCClassic #9656fcf GEOS-Chem and HEMCO submodule updates: Add GEOS-IT as meteorology option
GEOS-Chem #8dea9d5ab Bug fix: Use mol wt of atomic Hg for HgBr0 in Hg simulation
HEMCO     #6e2a808 Merge PR #214 (branch 'feature/update-transport-tracers') into dev/3.7.0

Number of execution tests: 5

Submitted as SLURM job: 59887244
==============================================================================
 
Execution tests:
------------------------------------------------------------------------------
gchp_merra2_fullchem................................Execute Simulation....PASS
gchp_merra2_fullchem_benchmark......................Execute Simulation....PASS
gchp_merra2_fullchem_RRTMG..........................Execute Simulation....PASS
gchp_merra2_tagO3...................................Execute Simulation....PASS
gchp_merra2_TransportTracers........................Execute Simulation....FAIL
 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 4
Execution tests failed: 1
Execution tests not yet completed: 0

msulprizio
msulprizio approved these changes Jun 28, 2023
View reviewed changes
Copy link
Contributor

@msulprizio msulprizio left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@yantosca Did you also want to add a comment to CHANGELOG.md for the added missing MW check? Otherwise looks good to merge.

@yantosca
Added sentence about error checking MW values to CHANGELOG.md
a91a684 
Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca yantosca mentioned this pull request Jun 28, 2023
Closed
4 tasks
@yantosca Octobox
Copy link
Contributor Author

@msulprizio: I have updated the CHANGELOG.md file now. Thanks for catching that!

@yantosca
Copy link
Contributor Author

yantosca commented Jul 5, 2023

Merged into dev/14.2.1; integration tests are running.

@yantosca
Copy link
Contributor Author

yantosca commented Jul 5, 2023 •
edited

GCClassic and GCHP TransportTracers execution tests failed because there is no MW_g value for the age of air species.

GEOS-Chem ERROR [0023]: MW_g for species aoa is undefined!
 --> LOCATION:  -> at Init_Species_Database (in module Headers/species_database_mod.F90

We can fix this problem by assigning MW_g: 1.0 for the various age of air species in the transport tracers simulations.

We will run integration tests again.

@yantosca
Copy link
Contributor Author

yantosca commented Jul 5, 2023

A few more TransportTracers species had missing molecular weights. We have set these to 1.0 and are retrying the integration tests once more.

@yantosca
Copy link
Contributor Author

yantosca commented Jul 6, 2023 •
edited

After merging this branch on top of PR #1794, All GEOS-Chem Classic integration tests passed (except TOMAS which is a known issue that will be fixed later):

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

GCClassic #8b373e5 Merge PR #41 (Update "test" symbolic link to int test root folder)
GEOS-Chem #be7f36703 Set missing MW_g values for more TransportTracers to 1.0
HEMCO     #faaddbb Merge PR #220 (branch 'feature/add_geosit_as_met_option') into dev/3.7.0

Using 24 OpenMP threads
Number of execution tests: 26

Submitted as SLURM job: 61476745
==============================================================================
 
Execution tests:
------------------------------------------------------------------------------
gc_05x0625_NA_47L_merra2_CH4........................Execute Simulation....PASS
gc_05x0625_NA_47L_merra2_fullchem...................Execute Simulation....PASS
gc_4x5_47L_merra2_fullchem..........................Execute Simulation....PASS
gc_4x5_47L_merra2_fullchem_TOMAS15..................Execute Simulation....FAIL
gc_4x5_47L_merra2_fullchem_TOMAS40..................Execute Simulation....FAIL
gc_4x5_merra2_aerosol...............................Execute Simulation....PASS
gc_4x5_merra2_carbon................................Execute Simulation....PASS
gc_4x5_merra2_CH4...................................Execute Simulation....PASS
gc_4x5_merra2_CO2...................................Execute Simulation....PASS
gc_4x5_merra2_fullchem..............................Execute Simulation....PASS
gc_4x5_merra2_fullchem_aciduptake...................Execute Simulation....PASS
gc_4x5_merra2_fullchem_APM..........................Execute Simulation....PASS
gc_4x5_merra2_fullchem_benchmark....................Execute Simulation....PASS
gc_4x5_merra2_fullchem_complexSOA...................Execute Simulation....PASS
gc_4x5_merra2_fullchem_complexSOA_SVPOA.............Execute Simulation....PASS
gc_4x5_merra2_fullchem_LuoWd........................Execute Simulation....PASS
gc_4x5_merra2_fullchem_marinePOA....................Execute Simulation....PASS
gc_4x5_merra2_fullchem_RRTMG........................Execute Simulation....PASS
gc_4x5_merra2_Hg....................................Execute Simulation....PASS
gc_4x5_merra2_metals................................Execute Simulation....PASS
gc_4x5_merra2_POPs_BaP..............................Execute Simulation....PASS
gc_4x5_merra2_tagCH4................................Execute Simulation....PASS
gc_4x5_merra2_tagCO.................................Execute Simulation....PASS
gc_4x5_merra2_tagO3.................................Execute Simulation....PASS
gc_4x5_merra2_TransportTracers......................Execute Simulation....PASS
gc_4x5_merra2_TransportTracers_LuoWd................Execute Simulation....PASS
 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 24
Execution tests failed: 2
Execution tests not yet completed: 0

Also, most integration tests (except for those with parallelization issues as described in #1682) are identical to PR #1794.

Checking gc_05x0625_NA_47L_merra2_CH4
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_05x0625_NA_47L_merra2_fullchem
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_47L_merra2_fullchem
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_47L_merra2_fullchem_TOMAS15
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_47L_merra2_fullchem_TOMAS40
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_aerosol
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_carbon
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_CH4
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_CO2
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_aciduptake
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_APM
   -> 3 differences found in OutputDir
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/HEMCO_diagnostics.201907010000.nc 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_fullchem_APM/OutputDir/HEMCO_diagnostics.201907010000.nc 
   -> 1 difference found in Restarts
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_fullchem_APM/Restarts/GEOSChem.Restart.20190701_0100z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_fullchem_APM/Restarts/GEOSChem.Restart.20190701_0100z.nc4 

Checking gc_4x5_merra2_fullchem_benchmark
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_complexSOA
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_complexSOA_SVPOA
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_LuoWd
   -> 3 differences found in OutputDir
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_fullchem_LuoWd/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_fullchem_LuoWd/OutputDir/GEOSChem.Metrics.20190701_0000z.nc4 
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_fullchem_LuoWd/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_fullchem_LuoWd/OutputDir/GEOSChem.SpeciesConc.20190701_0000z.nc4 
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_fullchem_LuoWd/OutputDir/HEMCO_diagnostics.201907010000.nc 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_fullchem_LuoWd/OutputDir/HEMCO_diagnostics.201907010000.nc 
   -> 1 difference found in Restarts
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_fullchem_LuoWd/Restarts/GEOSChem.Restart.20190701_0100z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_fullchem_LuoWd/Restarts/GEOSChem.Restart.20190701_0100z.nc4 

Checking gc_4x5_merra2_fullchem_marinePOA
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_fullchem_RRTMG
   -> 1 difference found in OutputDir
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_fullchem_RRTMG/OutputDir/GEOSChem.RRTMG.20190701_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_fullchem_RRTMG/OutputDir/GEOSChem.RRTMG.20190701_0000z.nc4 
   -> No differences in Restarts

Checking gc_4x5_merra2_Hg
   -> 4 differences found in OutputDir
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_Hg/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_Hg/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
diff -r GCC_14.2.1_r1/rundirs/gc_4x5_merra2_Hg/OutputDir/geoschem_species_metadata.yml GCC_14.2.1_r2/rundirs/gc_4x5_merra2_Hg/OutputDir/geoschem_species_metadata.yml
166a167
>   MW_g: 200.59
   -> 1 difference found in Restarts
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_Hg/Restarts/GEOSChem.Restart.20190101_0100z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_Hg/Restarts/GEOSChem.Restart.20190101_0100z.nc4 

Checking gc_4x5_merra2_metals
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_POPs_BaP
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_tagCH4
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_tagCO
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_tagO3
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gc_4x5_merra2_TransportTracers
   -> 19 differences found in OutputDir
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers/OutputDir/GEOSChem.AdvFluxVert.20190101_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers/OutputDir/GEOSChem.AdvFluxVert.20190101_0000z.nc4 
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers/OutputDir/GEOSChem.Budget.20190101_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers/OutputDir/GEOSChem.Budget.20190101_0000z.nc4 
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers/OutputDir/GEOSChem.CloudConvFlux.20190101_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers/OutputDir/GEOSChem.CloudConvFlux.20190101_0000z.nc4 
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
diff -r GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers/OutputDir/geoschem_species_metadata.yml GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers/OutputDir/geoschem_species_metadata.yml
181a182
>   MW_g: 1.0
197a199
>   MW_g: 1.0
213a216
>   MW_g: 1.0
283a287
>   MW_g: 1.0
299a304
>   MW_g: 1.0
315a321
>   MW_g: 1.0
332a339
>   MW_g: 1.0
   -> 1 difference found in Restarts
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers/Restarts/GEOSChem.Restart.20190101_0100z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers/Restarts/GEOSChem.Restart.20190101_0100z.nc4 

Checking gc_4x5_merra2_TransportTracers_LuoWd
   -> 19 differences found in OutputDir
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/OutputDir/GEOSChem.AdvFluxVert.20190101_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/OutputDir/GEOSChem.AdvFluxVert.20190101_0000z.nc4 
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/OutputDir/GEOSChem.Budget.20190101_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/OutputDir/GEOSChem.Budget.20190101_0000z.nc4 
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/OutputDir/GEOSChem.CloudConvFlux.20190101_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/OutputDir/GEOSChem.CloudConvFlux.20190101_0000z.nc4 
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
diff -r GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/OutputDir/geoschem_species_metadata.yml GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/OutputDir/geoschem_species_metadata.yml
181a182
>   MW_g: 1.0
197a199
>   MW_g: 1.0
213a216
>   MW_g: 1.0
283a287
>   MW_g: 1.0
299a304
>   MW_g: 1.0
315a321
>   MW_g: 1.0
332a339
>   MW_g: 1.0
   -> 1 difference found in Restarts
      * GCC_14.2.1_r1/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/Restarts/GEOSChem.Restart.20190101_0100z.nc4 
        GCC_14.2.1_r2/rundirs/gc_4x5_merra2_TransportTracers_LuoWd/Restarts/GEOSChem.Restart.20190101_0100z.nc4

NOTE: This update seems to fix an issue in the TransportTracers simulation where the missing MW_g value for certain species caused these species to be zero:

Using configuration file tt.yml
... Creating single-level plots
... Creating zonal mean plots
... Printing totals and differences
... Only showing variables with |absolute difference| > 0.0
Variable               Ref=GCC_14.2.1_r1        Dev=GCC_14.2.1_r2        Dev - Ref
SpeciesConcVV_aoa    : 0.0                    | 6506.6577              | 6506.65771484375 
SpeciesConcVV_aoa_bl : 0.0                    | 6517.903               | 6517.90283203125 
SpeciesConcVV_aoa_nh : 0.0                    | 6517.903               | 6517.90283203125 
SpeciesConcVV_nh_5   : 0.0                    | 0.00018181019          | 0.00018181018822360784 
SpeciesConcVV_nh_50  : 0.0                    | 0.00018226528          | 0.00018226528482045978 
SpeciesConcVV_st80_25 : 0.0                    | 0.00036442935          | 0.00036442934651859105 
SpeciesConcVV_stOX   : -8.978163e-08          | -4.4859515e-08         | 4.4922135344904746e-08

@yantosca
Copy link
Contributor Author

yantosca commented Jul 6, 2023 •
edited

After merging this branch on top of PR #1794, all GCHP integration tests passed:

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

GCClassic #76d9382 Merge PR #327 (Update "test" symbolic link to int test root folder)
GEOS-Chem #be7f36703 Set missing MW_g values for more TransportTracers to 1.0
HEMCO     #faaddbb Merge PR #220 (branch 'feature/add_geosit_as_met_option') into dev/3.7.0

Number of execution tests: 5

Submitted as SLURM job: 61476761
==============================================================================
 
Execution tests:
------------------------------------------------------------------------------
gchp_merra2_fullchem................................Execute Simulation....PASS
gchp_merra2_fullchem_benchmark......................Execute Simulation....PASS
gchp_merra2_fullchem_RRTMG..........................Execute Simulation....PASS
gchp_merra2_tagO3...................................Execute Simulation....PASS
gchp_merra2_TransportTracers........................Execute Simulation....PASS
 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 5
Execution tests failed: 0
Execution tests not yet completed: 0

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

NOTE: This update seems to fix an issue in the TransportTracers simulation where the missing MW_g value for certain species caused these species to be zero:

Checking gchp_merra2_fullchem
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_fullchem_benchmark
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_fullchem_RRTMG
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_tagO3
   -> No differences in OutputDir
   -> No differences in Restarts

Checking gchp_merra2_TransportTracers
   -> 18 differences found in OutputDir
      * GCHP_14.2.1_r1/rundirs/gchp_merra2_TransportTracers/OutputDir/GEOSChem.Budget.20190101_0000z.nc4 
        GCHP_14.2.1_r2/rundirs/gchp_merra2_TransportTracers/OutputDir/GEOSChem.Budget.20190101_0000z.nc4 
      * GCHP_14.2.1_r1/rundirs/gchp_merra2_TransportTracers/OutputDir/GEOSChem.CloudConvFlux.20190101_0000z.nc4 
        GCHP_14.2.1_r2/rundirs/gchp_merra2_TransportTracers/OutputDir/GEOSChem.CloudConvFlux.20190101_0000z.nc4 
      * GCHP_14.2.1_r1/rundirs/gchp_merra2_TransportTracers/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
        GCHP_14.2.1_r2/rundirs/gchp_merra2_TransportTracers/OutputDir/GEOSChem.SpeciesConc.20190101_0000z.nc4 
diff -r GCHP_14.2.1_r1/rundirs/gchp_merra2_TransportTracers/OutputDir/geoschem_species_metadata.yml GCHP_14.2.1_r2/rundirs/gchp_merra2_TransportTracers/OutputDir/geoschem_species_metadata.yml
181a182
>   MW_g: 1.0
197a199
>   MW_g: 1.0
213a216
>   MW_g: 1.0
283a287
>   MW_g: 1.0
299a304
>   MW_g: 1.0
315a321
>   MW_g: 1.0
332a339
>   MW_g: 1.0
   -> 1 difference found in Restarts
      * GCHP_14.2.1_r1/rundirs/gchp_merra2_TransportTracers/Restarts/GEOSChem.Restart.20190101_0100z.c24.nc4 
        GCHP_14.2.1_r2/rundirs/gchp_merra2_TransportTracers/Restarts/GEOSChem.Restart.20190101_0100z.c24.nc4

NOTE: This update seems to fix an issue in the TransportTracers simulation where the missing MW_g value for certain species caused these species to be zero:

Using configuration file tt.yml
... Creating single-level plots
... Creating zonal mean plots
Warning: zonal mean comparison must be lat-lon. Defaulting to 1x1.25
... Printing totals and differences
... Only showing variables with |absolute difference| > 0.0
Variable               Ref=GCHP_14.2.1_r1       Dev=GCHP_14.2.1_r2       Dev - Ref
SpeciesConcVV_aoa    : 0.0                    | 6786.1787              | 6786.1787109375 
SpeciesConcVV_aoa_bl : 0.0                    | 6793.295               | 6793.294921875 
SpeciesConcVV_aoa_nh : 0.0                    | 6793.295               | 6793.294921875 
SpeciesConcVV_nh_5   : 0.0                    | 0.00021571254          | 0.00021571254183072597 
SpeciesConcVV_nh_50  : 0.0                    | 0.00021625252          | 0.00021625251974910498 
SpeciesConcVV_st80_25 : 0.0                    | 0.0004323849           | 0.00043238489888608456

yantosca added a commit that referenced this pull request Jul 6, 2023
@yantosca
Assign aoa (age of air) species a dummy MW_g value of 1.0
51b8159 
run/shared/species_database.yml
- The updates in PR #1843 (add sanity check for missing MW_g) now
  causes the TransportTracers simulation to fail because the aoa
  (age of air) tracers do not have an assigned MW_g value.
- Setting the MW_g value to 1.0 for age of air species will allow
  the code to get past the error check for missing MW_g values when
  reading species metadata from "species_database.yml".

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
@yantosca yantosca merged commit b9ca774 into dev/14.2.1 Jul 6, 2023
@yantosca yantosca deleted the bugfix/prevent-zero-mw branch July 6, 2023 14:57
@yantosca yantosca mentioned this pull request Jul 6, 2023
Merged
1 task
@yantosca yantosca added this to the 14.2.1 milestone Jul 6, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@msulprizio msulprizio msulprizio approved these changes

Assignees

@yantosca yantosca

Labels
category: Feature Request New feature or request no-diff-to-benchmark This update will not change the results of fullchem benchmark simulations topic: Structural Modifications Related to GEOS-Chem structural modifications (as opposed to scientific updates)
Projects
None yet
Milestone
14.2.1
Development

Successfully merging this pull request may close these issues.

GEOS-Chem 13.3.0 memory error
2 participants
@yantosca @msulprizio