Add simulation with all diagnostics turned to integration testing #2399
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…RY.rc to GCClassic integration tests In order to evaluate all diagnostic collections, we now include a simulation with all collections activated in HISTORY.rc. This is a copy of the gc_4x5_merra2_fullchem_benchmark simulation with the comment character removed from all collection names at the top of HISTORY.rc. Signed-off-by: Melissa Sulprizio <mpayer@seas.harvard.edu>
1 task
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The all diagnostics run is currently failing integration tests: The error in the log file is: We will investigate and add fixes to this branch. |
msulprizio
added
topic: Benchmarking and Testing
run/GCClassic/HISTORY.rc.fullchem - Added missing fields for the UVFlux collection (frequency, duration, mode, fields). CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
test/shared/commonFunctionsForTests.sh - Update SED_HISTORY_RC_1 and SED_HISTORY_RC_N to use regex wildcard characters for certain digits - Update logic so that we first test on the resolution name before changing frequency & duration values to 20 mins (for nested-grid tests) or 1-hr (for other tests) run/GCClassic/HISTORY.rc.templates/HISTORY.rc.fullchem - Update frequency and duration of the TOMAS collection from "010000" to "00000100 000000", to be consistent with other collections Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
test/shared/commonFunctionsForTests.sh - Add "print_submodule_head_commits" function to print the commit hash & description at the head of each submodule test/integration/GCClassic/integrationTestCreate.sh test/integration/GCClassic/integrationTestCompile.sh test/integration/GCClassic/integrationTestExecute.sh test/integration/GCHP/integrationTestCreate.sh test/integration/GCHP/integrationTestCompile.sh test/integration/GCHP/integrationTestExecute.sh - Now call print_submodule_head_commits instead of using inlined code Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
test/shared/commonFunctionsForTests.sh - Remove "_GridComp" from the "FVdycoreCubed" submodule display name in function print_submodule_head_commits test/integration/GCHP/integrationTestCompile.sh test/integration/GCHP/integrationTestCreate.sh test/integration/GCHP/integrationTestExecute.sh - Now use an offset of 14 characters for print_submodule_head_commits Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
test/integration/GCHP/integrationTestCreate.sh - Removed "exit 1" statement that was leftover from debugging. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
test/integration/GCHP/integrationTestCreate.sh - Create a gchp_merra2_fullchem_alldiags by copying the gchp_merra2_fullchem_benchmark run directory and: - Disable RRTMG, Tomas, and DynHeating collections, as these are not enabled for fullchem_benchmark - Print the path of the gchp_merra2_fullchem_alldiags directory test/integration/GCClassic/integrationTestCreate.sh - Print the path of the gc_4x5_merra2_fullchem_alldiags directory - Also disable the DynHeating collection (if present) Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
GeosCore/planeflight_mod.F90 - Replace calls to GEOS_CHEM_STOP (which stops the run upon error) with calls to GC_Error + RETURN (to pass the error back to the main program). run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.* - Send planeflight diagnostic "plane.log" output to OutputDir - Now use dummy input file for ObsPack -- facilitates testing test/integration/GCClassic/integrationTestCreate.sh - Define bash variables to hold paths to configuration files (and unset them at the end of the script) - Navigate into the alldiags run directory to simplify bash commands - Copy the dummy planeflight and obspack input files to the run directory for the "alldiags" integration test - Call "toggle_geoschem_config_option" to turn on the planeflight and obspack diagnostics test/shared/alldiags/Planeflight.dat.20190701 - Dummy input file for the planeflight diagnostic used in the "alldiags" integration tests test/shared/commonFunctionsForTests.sh - Add comments to "print_submodule_head_commits" function - Add new function "toggle_geoschem_config_option" to toggle the "activate" value in the planeflight and obspack diagnostic menus in geoschem_config.yml CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.* - Change "obspack_dummy_input_for_testing.20190701.nc" to "obspack_input_for_testing.20190701.nc" in all GEOS-Chem Classic geoschem_config.yml templates. This will avoid an issue where "mm" is confused with minutes. Fix this issue later. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
test/shared/commonFunctionsForTests.sh
- Add the current directory (.) to the list of submodules for which
we will obtain Git commit hashes
- In the display name (y), replace "." with the basename of
argument ${2}. This is the name of the superproject.
Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
test/integration/GCClassic/integrationTestCreate.sh - Bug fix: We forgot to adjust the name of the sample ObsPack data file stored in the $obsPk variable. This has now been corrected. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
test/integration/GCClassic/integrationTestCreate.sh
- In the grep command used to define the extDataDir variable, we must
use ${HOME} instead of ~. Otherwise the grep fails. This was
causing the sample ObsPack data file not to be copied to the alldiags
test folder.
Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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All GEOS-Chem Classic integration tests passed: ==============================================================================
GEOS-Chem Classic: Execution Test Results
CodeDir : 67b58e6 GEOS-Chem submod update: Merge PR #2394 (Add GCAP int test)
GEOS-Chem : 03a25c37d Bug fix: Use ${HOME} instead of ~ in grep command
HEMCO : e68ebae HEMCO 3.9.2 release
Cloud-J : 37a4ece Update release version number and date
HETP : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables
Using 24 OpenMP threads
Number of execution tests: 29
Submitted as SLURM job: 41764773
==============================================================================
Execution tests:
------------------------------------------------------------------------------
...
gc_4x5_merra2_fullchem_alldiags.....................Execute Simulation....PASS
...
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 29
Execution tests failed: 0
Execution tests not yet completed: 0
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% All execution tests passed! %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%The alldiags test created these files: GEOSChem.AdvFluxVert.20190701_0000z.nc4 GEOSChem.ProdLoss.20190701_0000z.nc4
GEOSChem.AerosolMass.20190701_0000z.nc4 GEOSChem.RxnConst.20190701_0000z.nc4
GEOSChem.Aerosols.20190701_0000z.nc4 GEOSChem.RxnRates.20190701_0000z.nc4
GEOSChem.BoundaryConditions.20190701_0000z.nc4 GEOSChem.SatDiagn.20190701_0000z.nc4
GEOSChem.BoundaryConditions.20190701_0100z.nc4 GEOSChem.SatDiagnEdge.20190701_0000z.nc4
GEOSChem.Budget.20190701_0000z.nc4 GEOSChem.SpeciesConc.20190701_0000z.nc4
GEOSChem.CloudConvFlux.20190701_0000z.nc4 geoschem_species_metadata.yml
GEOSChem.ConcAboveSfc.20190701_0100z.nc4 GEOSChem.StateChm.20190701_0000z.nc4
GEOSChem.ConcAfterChem.20190701_0000z.nc4 GEOSChem.StateMet.20190701_0000z.nc4
GEOSChem.DryDep.20190701_0000z.nc4 GEOSChem.StratBM.20190701_0000z.nc4
GEOSChem.JValues.20190701_0000z.nc4 GEOSChem.UVFlux.20190701_0000z.nc4
GEOSChem.KppARDiags.20190701_0000z.nc4 GEOSChem.WetLossConv.20190701_0000z.nc4
GEOSChem.KppDiags.20190701_0000z.nc4 GEOSChem.WetLossLS.20190701_0000z.nc4
GEOSChem.LevelEdgeDiags.20190701_0000z.nc4 HEMCO_diagnostics.201907010000.nc
GEOSChem.Metrics.20190701_0000z.nc4 plane.log.20190701The ObsPack diagnostic output is: netcdf GEOSChem.ObsPack.20190701_0000z {
dimensions:
obs = UNLIMITED ; // (48 currently)
species = 3 ;
char_len_obs = 200 ;
variables:
char obspack_id(obs, char_len_obs) ;
obspack_id:long_name = "obspack_id" ;
obspack_id:units = "1" ;
obspack_id:_Storage = "chunked" ;
obspack_id:_ChunkSizes = 1, 200 ;
obspack_id:_NoFill = "true" ;
int nsamples(obs) ;
nsamples:long_name = "no. of model samples" ;
nsamples:units = "1" ;
nsamples:comment = "Number of discrete model samples in average" ;
nsamples:_Storage = "chunked" ;
nsamples:_ChunkSizes = 1024 ;
nsamples:_Endianness = "little" ;
nsamples:_NoFill = "true" ;
int averaging_interval(obs) ;
averaging_interval:long_name = "Amount of model time over which this observation is averaged" ;
averaging_interval:units = "seconds" ;
averaging_interval:_Storage = "chunked" ;
averaging_interval:_ChunkSizes = 1024 ;
averaging_interval:_Endianness = "little" ;
averaging_interval:_NoFill = "true" ;
int averaging_interval_start(obs) ;
averaging_interval_start:long_name = "Start of averaging interval" ;
averaging_interval_start:units = "seconds since 1970-01-01 00:00:00 UTC" ;
averaging_interval_start:calendar = "standard" ;
averaging_interval_start:_Storage = "chunked" ;
averaging_interval_start:_ChunkSizes = 1024 ;
averaging_interval_start:_Endianness = "little" ;
averaging_interval_start:_NoFill = "true" ;
int averaging_interval_end(obs) ;
averaging_interval_end:long_name = "End of averaging interval" ;
averaging_interval_end:units = "seconds since 1970-01-01 00:00:00 UTC" ;
averaging_interval_end:calendar = "standard" ;
averaging_interval_end:_Storage = "chunked" ;
averaging_interval_end:_ChunkSizes = 1024 ;
averaging_interval_end:_Endianness = "little" ;
averaging_interval_end:_NoFill = "true" ;
float lon(obs) ;
lon:long_name = "longitude" ;
lon:units = "degrees_east" ;
lon:_Storage = "chunked" ;
lon:_ChunkSizes = 1024 ;
lon:_Endianness = "little" ;
lon:_NoFill = "true" ;
float lat(obs) ;
lat:long_name = "latitude" ;
lat:units = "degrees_north" ;
lat:_Storage = "chunked" ;
lat:_ChunkSizes = 1024 ;
lat:_Endianness = "little" ;
lat:_NoFill = "true" ;
float u(obs) ;
u:long_name = "Zonal component of wind" ;
u:units = "m s^-1" ;
u:_Storage = "chunked" ;
u:_ChunkSizes = 1024 ;
u:_Endianness = "little" ;
u:_NoFill = "true" ;
float v(obs) ;
v:long_name = "Meridional component of wind" ;
v:units = "m s^-1" ;
v:_Storage = "chunked" ;
v:_ChunkSizes = 1024 ;
v:_Endianness = "little" ;
v:_NoFill = "true" ;
float blh(obs) ;
blh:long_name = "Boundary layer height" ;
blh:units = "m" ;
blh:_Storage = "chunked" ;
blh:_ChunkSizes = 1024 ;
blh:_Endianness = "little" ;
blh:_NoFill = "true" ;
float q(obs) ;
q:long_name = "mass_fraction_of_water_inair" ;
q:units = "g water (kg air)^-1" ;
q:_Storage = "chunked" ;
q:_ChunkSizes = 1024 ;
q:_Endianness = "little" ;
q:_NoFill = "true" ;
float pressure(obs) ;
pressure:long_name = "pressure" ;
pressure:units = "hPa" ;
pressure:_Storage = "chunked" ;
pressure:_ChunkSizes = 1024 ;
pressure:_Endianness = "little" ;
pressure:_NoFill = "true" ;
float temperature(obs) ;
temperature:long_name = "temperature" ;
temperature:units = "K" ;
temperature:_Storage = "chunked" ;
temperature:_ChunkSizes = 1024 ;
temperature:_Endianness = "little" ;
temperature:_NoFill = "true" ;
float CO(obs) ;
CO:long_name = "Carbon monoxide" ;
CO:units = "mol mol-1" ;
CO:_FillValue = -1.e+34f ;
CO:_Storage = "chunked" ;
CO:_ChunkSizes = 1024 ;
CO:_Endianness = "little" ;
CO:_NoFill = "true" ;
float NO(obs) ;
NO:long_name = "Nitrogen oxide" ;
NO:units = "mol mol-1" ;
NO:_FillValue = -1.e+34f ;
NO:_Storage = "chunked" ;
NO:_ChunkSizes = 1024 ;
NO:_Endianness = "little" ;
NO:_NoFill = "true" ;
float O3(obs) ;
O3:long_name = "Ozone" ;
O3:units = "mol mol-1" ;
O3:_FillValue = -1.e+34f ;
O3:_Storage = "chunked" ;
O3:_ChunkSizes = 1024 ;
O3:_Endianness = "little" ;
O3:_NoFill = "true" ;
// global attributes:
:history = "GEOS-Chem simulation at 2024/07/29 18:41" ;
:conventions = "CF-1.4" ;
:references = "www.geos-chem.org; wiki.geos-chem.org" ;
:model_start_date = "2019/07/01 00:00:00 UTC" ;
:model_end_date = "2019/07/01 01:00:00 UTC" ;
:_NCProperties = "version=2,netcdf=4.8.0,hdf5=1.10.7" ;
:_SuperblockVersion = 2 ;
:_IsNetcdf4 = 0 ;
:_Format = "netCDF-4 classic model" ;
data:
}and the Planeflight output is: POINT TYPE YYYYMMDD HHMM LAT LON PRESS OBS T-IND P-I I-IND J-IND TRA_001 TRA_002 O3 OH RO2 AN NOy GMAO_TEMP AODC_SULF AODB_SULF TIME_LT AQAER_RAD AQAER_SURF JVL_001
1 DC-8 20190701 0005 34.39 -95.00 757.33 9999.000 000000001 015 00018 00032 1.130E-009 1.711E-010 1.239E+012 8.618E+005 2.172E-011 1.117E-011 8.873E-010 2.855E+002 2.976E-002 2.788E-002 1.772E+001 1.162E-005 7.701E-008 3.905E-027
2 DC-8 20190701 0007 34.53 -95.08 668.89 9999.000 000000001 019 00018 00032 9.849E-010 8.714E-011 1.150E+012 1.015E+006 2.103E-011 8.928E-012 9.583E-010 2.789E+002 2.976E-002 2.839E-002 1.774E+001 8.989E-006 2.940E-008 1.609E-025
3 DC-8 20190701 0009 34.70 -95.16 574.40 9999.000 000000001 021 00018 00032 9.753E-010 6.904E-011 1.101E+012 1.038E+006 2.020E-011 8.802E-012 1.039E-009 2.731E+002 2.976E-002 2.852E-002 1.776E+001 8.067E-006 1.770E-008 2.169E-024
4 DC-8 20190701 0010 34.86 -95.26 484.89 9999.000 000000001 024 00018 00032 9.726E-010 5.282E-011 1.032E+012 1.302E+006 1.744E-011 8.728E-012 1.216E-009 2.626E+002 2.976E-002 2.878E-002 1.777E+001 7.396E-006 4.076E-008 1.207E-022
5 DC-8 20190701 0012 35.03 -95.35 433.15 9999.000 000000003 025 00018 00032 9.695E-010 4.951E-011 9.837E+011 9.055E+005 1.462E-011 8.671E-012 1.255E-009 2.582E+002 2.902E-002 2.821E-002 1.779E+001 7.279E-006 5.059E-008 3.449E-022
6 DC-8 20190701 0014 35.21 -95.46 428.34 9999.000 000000003 025 00018 00032 9.695E-010 4.951E-011 9.837E+011 9.055E+005 1.462E-011 8.671E-012 1.255E-009 2.582E+002 2.902E-002 2.821E-002 1.781E+001 7.279E-006 5.059E-008 3.449E-022
7 DC-8 20190701 0016 35.39 -95.56 428.38 9999.000 000000003 025 00018 00032 9.695E-010 4.951E-011 9.837E+011 9.055E+005 1.462E-011 8.671E-012 1.255E-009 2.582E+002 2.902E-002 2.821E-002 1.783E+001 7.279E-006 5.059E-008 3.449E-022
8 DC-8 20190701 0017 35.57 -95.67 428.47 9999.000 000000003 025 00018 00032 9.695E-010 4.951E-011 9.837E+011 9.055E+005 1.462E-011 8.671E-012 1.255E-009 2.582E+002 2.902E-002 2.821E-002 1.784E+001 7.279E-006 5.059E-008 3.449E-022
9 DC-8 20190701 0019 35.75 -95.78 428.47 9999.000 000000003 025 00018 00032 9.695E-010 4.951E-011 9.837E+011 9.055E+005 1.462E-011 8.671E-012 1.255E-009 2.582E+002 2.902E-002 2.821E-002 1.786E+001 7.279E-006 5.059E-008 3.449E-022
10 DC-8 20190701 0024 36.34 -95.95 428.52 9999.000 000000003 025 00018 00033 6.711E-010 1.786E-011 1.125E+012 1.258E+006 6.137E-012 3.256E-012 2.211E-009 2.578E+002 1.675E-002 1.319E-002 1.791E+001 0.000E+000 0.000E+000 5.270E-022
11 DC-8 20190701 0026 36.53 -95.99 428.31 9999.000 000000003 025 00018 00033 6.711E-010 1.786E-011 1.125E+012 1.258E+006 6.137E-012 3.256E-012 2.211E-009 2.578E+002 1.675E-002 1.319E-002 1.793E+001 0.000E+000 0.000E+000 5.270E-022
12 DC-8 20190701 0028 36.73 -96.01 428.36 9999.000 000000003 025 00018 00033 6.711E-010 1.786E-011 1.125E+012 1.258E+006 6.137E-012 3.256E-012 2.211E-009 2.578E+002 1.675E-002 1.319E-002 1.795E+001 0.000E+000 0.000E+000 5.270E-022
13 DC-8 20190701 0030 36.93 -96.00 428.75 9999.000 000000003 025 00018 00033 6.711E-010 1.786E-011 1.125E+012 1.258E+006 6.137E-012 3.256E-012 2.211E-009 2.578E+002 1.675E-002 1.319E-002 1.797E+001 0.000E+000 0.000E+000 5.270E-022
14 DC-8 20190701 0031 37.09 -96.14 428.42 9999.000 000000005 025 00018 00033 6.701E-010 1.793E-011 1.124E+012 7.785E+005 5.736E-012 3.251E-012 2.218E-009 2.579E+002 1.668E-002 1.313E-002 1.798E+001 0.000E+000 0.000E+000 3.766E-022
15 DC-8 20190701 0033 37.25 -96.28 428.45 9999.000 000000005 025 00018 00033 6.701E-010 1.793E-011 1.124E+012 7.785E+005 5.736E-012 3.251E-012 2.218E-009 2.579E+002 1.668E-002 1.313E-002 1.800E+001 0.000E+000 0.000E+000 3.766E-022
16 DC-8 20190701 0035 37.41 -96.41 428.55 9999.000 000000005 025 00018 00033 6.701E-010 1.793E-011 1.124E+012 7.785E+005 5.736E-012 3.251E-012 2.218E-009 2.579E+002 1.668E-002 1.313E-002 1.802E+001 0.000E+000 0.000E+000 3.766E-022
17 DC-8 20190701 0037 37.57 -96.55 428.55 9999.000 000000005 025 00018 00033 6.701E-010 1.793E-011 1.124E+012 7.785E+005 5.736E-012 3.251E-012 2.218E-009 2.579E+002 1.668E-002 1.313E-002 1.804E+001 0.000E+000 0.000E+000 3.766E-022
18 DC-8 20190701 0038 37.72 -96.69 428.50 9999.000 000000005 025 00018 00033 6.701E-010 1.793E-011 1.124E+012 7.785E+005 5.736E-012 3.251E-012 2.218E-009 2.579E+002 1.668E-002 1.313E-002 1.805E+001 0.000E+000 0.000E+000 3.766E-022
19 DC-8 20190701 0040 37.88 -96.83 433.37 9999.000 000000005 025 00018 00033 6.701E-010 1.793E-011 1.124E+012 7.785E+005 5.736E-012 3.251E-012 2.218E-009 2.579E+002 1.668E-002 1.313E-002 1.807E+001 0.000E+000 0.000E+000 3.766E-022
20 DC-8 20190701 0042 38.02 -96.96 508.21 9999.000 000000005 023 00018 00033 6.319E-010 1.467E-011 1.273E+012 6.847E+005 6.338E-012 2.529E-012 2.246E-009 2.662E+002 1.668E-002 1.281E-002 1.809E+001 0.000E+000 0.000E+000 2.577E-023
21 DC-8 20190701 0044 38.16 -97.08 547.75 9999.000 000000005 022 00018 00033 6.072E-010 1.436E-011 1.330E+012 6.580E+005 7.058E-012 2.275E-012 2.055E-009 2.699E+002 1.668E-002 1.267E-002 1.811E+001 0.000E+000 0.000E+000 6.806E-024
22 DC-8 20190701 0045 38.29 -97.21 592.62 9999.000 000000005 020 00018 00033 5.642E-010 1.855E-011 1.366E+012 6.438E+005 8.849E-012 2.039E-012 1.892E-009 2.769E+002 1.668E-002 1.228E-002 1.812E+001 7.399E-006 3.245E-008 4.927E-025
23 DC-8 20190701 0047 38.38 -97.36 678.79 9999.000 000000005 018 00018 00033 5.716E-010 2.860E-011 1.389E+012 6.032E+005 9.921E-012 1.989E-012 1.705E-009 2.821E+002 1.668E-002 1.210E-002 1.814E+001 7.897E-006 3.401E-008 4.343E-026
24 DC-8 20190701 0049 38.46 -97.50 754.43 9999.000 000000005 015 00018 00033 6.411E-010 5.666E-011 1.450E+012 5.037E+005 1.155E-011 3.501E-012 1.595E-009 2.874E+002 1.668E-002 1.189E-002 1.816E+001 8.736E-006 4.730E-008 3.184E-027All GCClassic integration tests were zero-diff w/r/t PR #2394, except:
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The GCHP "alldiags" integration test fails with this error: GEOS-Chem ERROR [0006]: The mapData%slot2Id array corresponding to collection "BudgetWetDepFull" contains missing values! This can indicate that this collection is either undefined or turned off. Please check the HISTORY.rc configuration file in your run directory.
--> LOCATION: -> at Get_Mapping (in module Headers/state_diag_mod.F90)
GEOS-Chem ERROR [0006]: Error encountered in "Get_Mapping": BudgetWetDepFull
--> LOCATION: -> at Get_MapData_and_NumSlots (in module Headers/state_diag_mod.F90)
GEOS-Chem ERROR [0006]: Error encountered in "Get_MapData_and_NumSlots"!
--> LOCATION: -> at Init_and_Register_R8_3D (in module Headers/state_diag_mod.F90)
GEOS-Chem ERROR [0006]: Error encountered in "Init_and_Register", diagID =BudgetWetDepFull
--> LOCATION: -> at Init_State_Diag (in Headers/state_diag_mod.F90)
GEOS-Chem ERROR [0006]: Error encountered within call to "Init_State_Diag"!
--> LOCATION: -> at GC_Init_StateObj (in GeosCore/gc_environment_mod.F90)
pe=00006 FAIL at line=00255 gchp_chunk_mod.F90 <Error calling GC_Init_StateObj>
pe=00006 FAIL at line=01498 Chem_GridCompMod.F90 <status=1>
pe=00006 FAIL at line=01807 MAPL_Generic.F90 <status=1>We are investigating further. |
run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem - Now use SO4 instead of O3 for the Budget collection diagnostic fields. This will allow us to test The BudgetWetDep diagnostic, as SO4 is soluble and O3 is not. Using O3 caused a runtime error, which should now be fixed. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
test/integration/GCHP/integrationTestExecute.sh - Add an sed command to reset the cap_restart time to 000000 UTC. This will make sure that we restart the run from 0h UTC when we manually restart tests with utils/redoIntegrationTestExecute.sh. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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The GCHP error is due to the fact that the budget diagnostic used O3 as the sample species in the Budget.fields: 'BudgetWetDepFull_O3 ', 'GCHPchem',
'BudgetChemistryFull_O3 ', 'GCHPchem',
'BudgetConvectionFull_O3 ', 'GCHPchem',
'BudgetMixingFull_O3 ', 'GCHPchem',
'BudgetEmisDryDepFull_O3 ', 'GCHPchem',
#
'BudgetWetDepLevs1to35_O3 ', 'GCHPchem',
'BudgetChemistryLevs1to35_O3 ', 'GCHPchem',
'BudgetConvectionLevs1to35_O3 ', 'GCHPchem',
'BudgetMixingLevs1to35_O3 ', 'GCHPchem',
'BudgetEmisDryDepLevs1to35_O3 ', 'GCHPchem',
#
'BudgetWetDepTrop_O3 ', 'GCHPchem',
'BudgetChemistryTrop_O3 ', 'GCHPchem',
'BudgetConvectionTrop_O3 ', 'GCHPchem',
'BudgetMixingTrop_O3 ', 'GCHPchem',
'BudgetEmisDryDepTrop_O3 ', 'GCHPchem',
#
'BudgetWetDepPBL_O3 ', 'GCHPchem',
'BudgetChemistryPBL_O3 ', 'GCHPchem',
'BudgetConvectionPBL_O3 ', 'GCHPchem',
'BudgetMixingPBL_O3 ', 'GCHPchem',
'BudgetEmisDryDepPBL_O3 But O3 is not water-soluble, and thus does not have a wet deposition ID. The We have now changed the sample species from O3 to SO4, which is water soluble. |
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Another GCHP error was revealed by the "alldiags" test: GEOS-Chem ERROR [0010]: Could not find bin index for tag name: 574NM
--> LOCATION: -> at Get_UVFlux_Index (in module Headers/state_diag_mod.F90)
GEOS-Chem ERROR [0010]: Error encountered in routine "Get_UVFlux_Bin"!
--> LOCATION: -> at Get_Mapping (in module Headers/state_diag_mod.F90)@lizziel and I have traced it to routine ! Get the index for the tagname
DO N = 1, 18
IF ( TRIM( tagName ) == TRIM( UVFlux_Tag_Names(N) ) ) THEN
bin = N
EXIT
ENDIF
ENDDO
! Trap potential errros
IF ( bin < 0 ) THEN
errMsg = 'Could not find bin index for tag name: ' // TRIM( tagName )
CALL GC_Error( errMsg, RC, thisLoc )
RETURN
ENDIFThe error is that tagName is has |
Headers/state_diag_mod.F90 - In routine "Get_UVFLux_Bin", make sure that tagName and UVFlux_Tag_Names(N) are both in uppercase before comparing them for equality. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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Encountered yet another error in the GCHP alldiags test. I think the job ran out of memory. I bumped up the requested memory to 450000 GB and will see if that goes |
Interfaces/GCHP/gchp_historyexportsmod.F90 - Replace "informative message here" with a detailed error message. run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem - Uncomment the StratBM diagnostic entries test/integration/GCHP/integrationTestExecute.sh - Add a sed command to comment out the StratBM collection in the collections list of HISTORY.rc for the GCHP "alldiags" test CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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The issue was not the job running out of memory, but the StratBM diagnostic entries were commented out. I've uncommented those entries but have disabled the StratBM collection for the GCHP alldiags test, as that is only needed |
9 tasks
run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem - Fix typo (i.e. "DryDepACET" -> "DryDep_ACET") in the DryDep collection entries. This was causing a GCHP runtime error. test/integration/GCHP/integrationTestCreate.sh - Reactivate the StratBM collection, this should be OK. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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Found that the GCHP DryDep collection entries had a bunch of missing |
run/GCHP/HISTORY.rc.fullchem - Comment out (with `###` the Emissions diagnostic entries that are are also commented out in the corresponding HEMCO_Diagn.rc.fullchem template. This will disable them in the GCHP "alldiags" test. test/integration/GCClassic/integrationTestCreate.sh test/integration/GCHP/integrationTestCreate.sh - Disable the UVFlux collection in the "alldiags" integration test, as this is currently problematic. Look to fix this later. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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Also pushed the following updates:
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run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem - Added an extra # (now '####') when commenting out the unused diagnostic entries in the Emissions collection. This is needed for the "alldiags" test, which strips the first 3 '###' chars. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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After adding all of the above-mentioned fixes, all GCHP integration tests now pass: ==============================================================================
GCHP: Execution Test Results
CodeDir : 2d1bc44 GEOS-Chem submod update: Merge PR #2394 (Add GCAP int test)
MAPL : 231d53c Merge pull request #36 from geoschem/feature/improve_hflux_regridding
GMAO_Shared : 4ddb3ec Merge pull request #2 from geoschem/feature/mapl-upgrade
ESMA_cmake : ad5deba Added ecbuild as a submodule of ESMA_cmake
gFTL-shared : 4b82492 Merge branch 'upstream_v1.5.0' into feature/v1.5.0
FMS : 259759d Merge pull request #3 from geoschem/feature/update_gmao_libs
FVdycoreCubed : af42462 Merge PR #8 (Add PLEadv diagnostic for offline advection in GCHP)
geos-chem : ee5a477e6 Add an extra "#" to commented-out emission diagnostics
HEMCO : e68ebae HEMCO 3.9.2 release
yaFyaml : 19afe50 Merge branch 'upstream_v1.0.4' into feature/v1.0.4
pFlogger : 2c4b724 Merge branch 'upstream_v1.9.1' into feature/v1.9.1
Cloud-J : 37a4ece Update release version number and date
HETP : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables
Number of execution tests: 12
Submitted as SLURM job: 42064039
==============================================================================
...
gchp_merra2_fullchem_alldiags.......................Execute Simulation....PASS
...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% All execution tests passed! %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%All tests were zero-diff w/r/t PR #2394. |
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@msulprizio: GitHub wouldn't let me add you as a reviewer since this was originally your PR. But please do feel free to submit a review. |
msulprizio
commented
Aug 1, 2024
There was a problem hiding this comment.
This looks good to me @yantosca. Thanks for resolving these issues! I have one minor comment in the CHANGELOG but pending that this is good for merging.
CHANGELOG.md - Added "and GCHP" to the "Added simulation with all diagnostics..." sentence. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
yantosca
approved these changes
Aug 1, 2024
|
@lizziel @msulprizio: I merged (locally) into dev/no-diff-to-benchmark and reran integration tests. All tests passed and were zero-diff w/r/t the prior PR (#2394). |
yantosca
pushed a commit
that referenced
this pull request
Aug 5, 2024
This rebase brings the "feature/trop-prs-in-satdiagn" branch (which contains an update by @eamarais to add tropopause pressure to the SatDiagn collection) into the "dev/no-diff-to-benchmark" branch atop PR #2399. The original update was based off version 14.1.0. This merge brings PR # ( , by @) into Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This was referenced Aug 13, 2024
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Name and Institution (Required)
Name: Melissa Sulprizio
Institution: Harvard
Describe the update
In order to evaluate all diagnostic collections, we now include a simulation with all collections activated in HISTORY.rc. This is currently a copy of the
gc_4x5_merra2_fullchem_benchmarksimulation with the comment character removed from all collection names at the top ofHISTORY.rcwith the namegc_4x5_merra2_fullchem_alldiags.Still to do:
geoschem_config.ymlfor GCClassic testExpected changes
This is a zero diff update with respect to benchmark simulations.
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