Fix GEOS-Chem 14.5.0 build in CESM by excluding hard dependencies on HEMCO #2542
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Fix bug where download_data.py failed if the dryrun log filename contained uppercase characters e.g. 'Log.dryrun'. The solution is to not coerce the dryrun log filename to lowercase.
…HEMCO In the CESM model, emissions through HEMCO are provided to GEOS-Chem through the physics buffer and not through the HEMCO subroutine calls. A side-effect of this implementation is that HEMCO versions and GEOS-Chem versions in CESM can be decoupled, and thus hard-dependencies on HEMCO data structures should not apply. In this particular case, additional ExtState fields in HEMCO are causing CESM build failures in the latest GEOS-Chem version. Most (but not all) subroutines in hco_interface_gc_mod.F90 are unused in CESM and are now blocked off from MODEL_CESM to avoid this hard dependency. Signed-off-by: Haipeng Lin <hplin@seas.harvard.edu>
yantosca
added
category: Interface to External Model
yantosca
requested changes
Oct 31, 2024
Headers/state_diag_mod.F90 - Added State_Diag%SatDiagnEdgeCount counter for SatDiagnEdge collection - Added State_Diag%Archive_SatDiagnEdgeCount logical - Added State_Diag%Archive_SatDiagnEdge logical - Allocated State_Diag%SatDiagnPEDGE with vertical dimension State_Grid%NZ+1 instead of State_Grid%NZ GeosCore/diagnostics_mod.F90 - Initialize the State_Diag%SatDiagnEdgeCount counter in the DO loop where local time is updated for satellite diagnostics - Now use State_Grid%NZ+1 vertical levels when saving into the State_Diag%SatDiagnPedge field History/history_util_mod.F90 - Added routine "SatDiagn_or_SatDiagnEdge" to set logical flags to determine if the current container is either SatDiagn or SatDiagnEdge History/history_netcdf_mod.F90 - Call routine SatDiagn_or_SatDiagnEdge to set logical flags indicating if the current collection is SatDiagn or SatDiagnEdge - Added an IF block to compute the average of fields belonging to the SatDiagnEdge collection History/history_mod.F90 - Call routine SatDiagn_or_SatDiagnEdge to set logical flags indicating if the current collection is SatDiagn or SatDiagnEdge - Only reset State_Diag%SatDiagnCount to zero if the current collection is "SatDiagn" - Only reset the "State_Diag%SatDiagnEdgeCount" counter if the current collection is "SatDiagnEdge" CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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Thanks @yantosca, changelog updated! |
lizziel
reviewed
Nov 1, 2024
lizziel
approved these changes
Nov 1, 2024
msulprizio
changed the base branch from
dev/14.5.0
to
dev/no-diff-to-benchmark
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Note that I have changed the base branch to |
CHANGELOG.md - Updated with info about the satellite diagnostic fixes Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This issue happens with Intel 2022.2.1 and possibly others. Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
This merge brings PR geoschem#2560 (Fix trace metals simulation name in config file comments, by @ihough) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR fixes incorrect comments in configuration files. Also, merge conflicts in CHANGELOG.md have been resolved. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.ed
This merge brings PR # (Bug fix: allow uppercase log filename in download_data.py, by @ihough) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR adds a fix so that dry-run log file names that are fed to the download_data.py script can have mixed case. Merge conflicts in CHANGELOG.md have also been resolved. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR geoschem#2532 (Add allocate guards for arrays in pressure_mod, by @jwallwork) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR adds checks to make sure that we do not allocate arrays that have already been allocated. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR geoschem#2544 (Add counter for SatDiagnPedge collection; Prevent satelli-te diagnostic counters from being inadvertently reset, by @) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR does the following: 1. Adds a separate local time counter (State_Diag%SatDiagnEdgeCount) for the SatDiagnEdge collection 2. Allocates the State_Diag%SatDiagnPEDGE field with State_Diag%NZ+1 vertical levels. (This formerly was allocated with State_Diag%NZ levels, which cut off the top-of-the atmosphere (L=73) level). 3. Adds a new function SatDiagn_or_SatDiagnEdge in History/history_netcdf_mod.F90 to set logical flags to denote if the current container name is either "SatDiagn" or "SatDiagnEdge" 4. Added code in History/history_netcdf_mod.F90 to compute time-averages of fields belonging to the SatDiagnEdge collection. 5. Updated code in History/history_mod.F90 to: - Reset the State_Diag%SatDiagnCount counter array ONLY IF the current container name is SatDiagn. - Reset the State_Diag%SatDiagnEdgeCount counter array ONLY IF the current container name is SatDiagnEdge. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/shared/species_database.yml - Removed the duplicate WD_RetFactor YAML tag for HgClHO2 CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR geoschem#2580 (Remove duplicate WD_RetFactor tag for HgClHO2 entry in species-database.yml, by @yantosca) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR removes a duplicate YAML tag in the species database file. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR geoschem#2486 (Prevent segmentation fault in qfyaml with some compilers, by @lizziel) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR fixes a seg fault in Headers/qfyaml_mod.F90 that has been observed with certain compilers. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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@jimmielin: Is it OK if I push resolved merge conflicts back to your branch? This will also bring in the 14.5.0 updates. Just want to make sure that is OK w/ you (and that you're not actively using this branch). |
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@yantosca, looks like this branch has no merge conflicts so should be good to merge. |
This merge brings PR geoschem#2542 (Fix GEOS-Chem 14.5.0 build in CESM by excluding hard dependencies on HEMCO, by @jimmielin) into the GEOS-Chem "no-diff-to-benchmark" development stream. This PR removes hard-dependencies on HEMCO when building GEOS-Chem in the CESM ESM. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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All GEOS-Chem Classic integration tests passed, except for tagCO (known restart file issue) ==============================================================================
GEOS-Chem Classic: Execution Test Results
CodeDir : a8aeb02 GEOS-Chem update: Merge PR #2578 (Fixes for GCHP adjoint )
GEOS-Chem : 62f3db08b Merge PR #2578 (Fixes to compile GCHP adjoint)
HEMCO : deaa192 HEMCO 3.10.0 release
Cloud-J : f8a2b7f Update version number for 8.0.1 release
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: 59103476
==============================================================================
...
gc_4x5_merra2_tagCO.................................Execute Simulation....FAIL
...
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 29
Execution tests failed: 1
Execution tests not yet completed: 0Also all tests were zero-diff w/r/t the previous integration test except for:
|
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All GCHP integration tests passed: ==============================================================================
GCHP: Execution Test Results
CodeDir : 7c2d8e2 GEOS-Chem update: Merge PR #2578 (Fixes for GCHP adjoint )
MAPL : 9ad63ae Merge PR #37 containing update to vertically flip imports with dimensionless pressure proxy lev coordinates
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 : 62f3db08b Merge PR #2578 (Fixes to compile GCHP adjoint)
HEMCO : deaa192 HEMCO 3.10.0 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 : f8a2b7f Update version number for 8.0.1 release
HETP : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables
Number of execution tests: 12
Submitted as SLURM job: 59103750
==============================================================================
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% All execution tests passed! %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Also, all tests were zero-diff w/r/t the previous set of integration tests. |
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Name and Institution (Required)
Name: Haipeng Lin
Institution: Harvard Univ.
Describe the update
In the CESM model, emissions through HEMCO are provided to GEOS-Chem through the physics buffer and not through the HEMCO subroutine calls. A side-effect of this implementation is that HEMCO versions and GEOS-Chem versions in CESM can be decoupled, and thus hard-dependencies on HEMCO data structures should not apply.
In this particular case, additional ExtState fields in HEMCO are causing CESM build failures in the latest GEOS-Chem version. Most (but not all) subroutines in hco_interface_gc_mod.F90 are unused in CESM and are now blocked off from MODEL_CESM to avoid this hard dependency.
Note:
HCOI_GC_WriteDiagnwas rearranged in the module but otherwise unchanged, in order to use one#if !defined( MODEL_CESM )Expected changes
None
Reference(s)
N/A
Related Github Issue
Building CESM with latest GEOS-Chem tag
14.5.0-rc.0