KPP standalone interface from Obin Sturm #2482
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added 12 commits
September 26, 2024 14:44
lizziel
added
category: Feature Request
Signed-off-by: Lizzie Lundgren <[email protected]>
|
Hi Lizzie, thanks for getting this started! I'm still working on redoing a few c360 runs with the new compute resources on Discover before we can write up the manuscript about this tool and species-level tolerances. I will keep you all posted when that's out as a preprint, and thanks again for moving this PR upstream |
yantosca
added
the
topic: Chemical Mechanisms
lizziel
changed the base branch from
dev/14.5.0
to
dev/no-diff-to-benchmark
run/shared/kpp_standalone_interface.yml - Fixed typo: "output_dir" -> "output_directory" Signed-off-by: Bob Yantosca <[email protected]>
GeosCore/fullchem_mod.f90 - Use keyword arguments, for clarity GeosCore/kpp_standalone_interface.F90 - Remove Active_Cell and Active_Cell_Name from KPP_Standalone_YAML - Add new derived type KPP_Standalone_ActiveCell_Type, which is now declared with !$OMP THREADPRIVATE. This contains the Active_Cell and Active_Cell_Name fields. - Added new variable KPP_Standalone_ActiveCell, based on new KPP_Standalone_ActiveCell_Type NOTE: The KPP_Standalone_YAML is initialized outside of a parallel loop, so it does not need to be declared !$OMP THREADPRIVATE. But the choice of whether an (I,J,L) location corresponds to one of the "active_cells" (listed in the kpp_standalone_interface.yml file) happens within a parallelized loop. Thus we need to move the Active_Cell and Active_Cell_Name fields out of KPP_Standalone_YAML and into KPP_Standalone_ActiveCell. Signed-off-by: Bob Yantosca <[email protected]>
run/GCClassic/createRunDir.sh
- Copy run/shared/kpp_standalone_interface.yml to fullchem rundirs
run/shared/cleanRunDir.sh
- Skip removing bpch files (and {diag,tracer}info.dat files), we no
longer generate bpch output
- Add comments and usage examples
- Remove all fort.* files
- Remove OututDir/*.txt files as well (these are KPP standalone
interface files)
CHANGELOG.md
- Updated accordingly
Signed-off-by: Bob Yantosca <[email protected]>
.gitignore - Also ignore *.exe files GeosCore/fullchem_mod.F90 - Remove State_Grid from call to Check_ActiveCell GeosCore/kpp_standalone_interface.F90 - Updated subroutine header comments - Added cosmetic changes for clarity (mostly making code fit within 80 characters, for better readability) - Removed Active_Cell and Active_Cell_name from the KPP_Standalone_Interface_Type (should have been done previously) - Remove State_Grid argument from Check_ActiveCell, this was only used for debugging. Also removed commented out debug prints. - Use Format statements with write statments where expedient - Echo a message when the KPP standalone interface is manually disabled (i.e. when settings:activate = false) - Added display of location names and lon/lats at end of the routine Config_KPP_Standalone - In routine Write_Samples, wrap file I/O in an !$OMP CRITICAL block, in order to prevent more than one thread from writing to each file. - Removed RETURN statement from within !$OMP CRITICAL block, this is not allowed. - Bug fix: Write Kpp_Standalone_ActiveCell%Active_Cell_Name to file, and not Kpp_Standalone_YAML%Active_Cell_Name (which has been removed). Signed-off-by: Bob Yantosca <[email protected]>
GeosCore/kpp_standalone_interface.F90 - Moved to kppsa_interface_mod.F90 GeosCore/kppsa_interface_mod.F90 - Moved from kpp_standalone_interface - Renamed types, variables and routines using "KppSa" prefix: - KPP_Standalone_Interface_Type -> KppSa_Interface_Type - KPP_Standalone_ActiveCell_Type -> KppSa_ActiveCell_Type - KPP_Standalone_YAML -> KppSa_State - KPP_Standalone_ActiveCell -> KppSa_ActiveCell - Check_Domain -> KppSa_Check_Domain - Check_ActiveCell -> KppSa_Check_ActiveCell - Config_KPP_Standalone -> KppSa_Config - Write_Samples -> KppSa_Write_Samples - Cleanup_KPP_Standalone -> KppSa_Cleanup - Added KppSa_Check_Time function to determine if it is time to write KPP standalone output. This allows you to only write output e.g. at the end of a run instead of for each timestep. - Added KppSa_State%SkipWriteAtThisTime field, which is used to determine if we need to exit a routine early. GeosCore/fullchem_mod.F90 - "USE Kpp_Standalone_Interface" -> "USE KppSa_Interface_Mod" - Call renamed routines from kppsa_interface_mod.F90 - Now call KppSa_Check_Domain only if it is the first call to DO_FULLCHEM. This is to avoid repeated computations. - Now call KppSa_Check_Time to determine if we are in the time window when the model state should be archived to disk. - Updated comments and comment headers run/shared/kpp_standalone_interface.yml - Added "start_output_at" to denote starting date time for archiving model state - Added "stop_output_at" to denote ending date time for archiving model state - Updated comments CHANGELOG.md GeosCore/CMakeLists.txt - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
GeosCore/kppsa_interface_mod.F90
- In routine KppSa_Check_Time:
- rRmoved leftover debug print statements
- In routine Kpp_Check_ActiveCell
- Added an IF statement to exit after setting KppSa_State%Active_Cell to .FALSE.
and KppSa_Active_Cell_Name to '' if we are outside of the time
window specified in the kpp_standalone_interface.yml fiel.
- This will ensure that we only archive model state to disk during
the specified time window, which helps with computatonal efficiency.
- In routine KppSa_Config:
- Now write starting & ending date of archival window to log file
Signed-off-by: Bob Yantosca <[email protected]>
run/GCHP/createRunDir.sh - Added an if statement to copy run/shared/kpp_standalone_interface.yml to GCHP fullchem run directories (any option) Signed-off-by: Bob Yantosca <[email protected]>
obin1
reviewed
Oct 10, 2024
|
@obin1 @lizziel: FYI I have also modified this PR to save out the Now that we have per-species ATOL settings in GEOS-Chem 14.5.0, I will add another fix to save that out. This will be needed to set the ATOL for family/dummy species to a high value so as to keep them out of the error norm computations. |
GeosCore/fullchem_mod.F90 - Pass KPP integrator arguments ICNTRL and RCNTRL to KppSa_Write_Samples so that we can include it in the KPP standalone output. Signed-off-by: Bob Yantosca <[email protected]>
GeosCore/CMakeLists.txt - Changed permission from chmod 755 to chmod 644 GeosCore/kppsa_interface_mod.F90 - Now accept ICNTRL and RCNTRL as inputs to routine KppSa_Write_Samples - Change number of header lines from 48 to 60 - Better separate Meteorological metadata and KPP parameters for readability - Write out ICNTRL as 2 lines of format 10i6 - Write out RCNTRL as 4 lines of format 5f13.6 - Changed format e25.16e3 to es25.16e3, which changes the output from e.g. 0.5e1 to 5.0e0, etc., which is more standard - Write out ATOL after the species concentration with format es10.2e2 - Cosmetic changes (indentation, comments) Signed-off-by: Bob Yantosca <[email protected]>
GeosCore/kppsa_interface_mod.F90 - In routine KppSa_Write_Samples: - Added a "," in between the concentration and abs tolerance output - Simplified FORMAT statements 120 and 130 - Added FORMAT statements 140 and 150 Signed-off-by: Bob Yantosca <[email protected]>
yantosca
changed the base branch from
dev/no-diff-to-benchmark
to
dev/14.6.0
yantosca
approved these changes
Nov 20, 2024
|
All GCClassic integration tests passed: ==============================================================================
GEOS-Chem Classic: Execution Test Results
CodeDir : 0ecd8fa GEOS-Chem update: Merge PR #2507 (Fix CEDS TMB emissions)
GEOS-Chem : a86303771 Merge PR #2482 (KPP standalone interface from Obin Sturm)
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: 58916604
==============================================================================
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% All execution tests passed! %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Also all tests were zero-diff w/r/t 14.6.0-alpha.0 except for
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|
All GCHP integration tests passed: ==============================================================================
GCHP: Execution Test Results
CodeDir : 15de6b3 GEOS-Chem update: Merge PR #2507 (Fix CEDS TMB emissions)
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 : a86303771 Merge PR #2482 (KPP standalone interface from Obin Sturm)
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: 58926494
==============================================================================
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% All execution tests passed! %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%All tests were zero-diff w/r/t 14.6.0-alpha.1 |
yantosca
added a commit
that referenced
this pull request
Nov 22, 2024
This merge brings PR #2482 (KPP standalone interface from Obin Sturm, by @lizziel) into the GEOS-Chem 14.5.1 development stream. This PR brings the interface for the KPP standalone box model into GEOS-Chem 14.6.0. A new kpp_standalone_interface.yml file is placed into the run directory. In this YAML file, the user can select the locations and times for archiving model state to text files that can be fed into the KPP standalone model. Also the writing of files is now done in a thread-safe manner. Signed-off-by: Bob Yantosca <[email protected]>
This was referenced Nov 22, 2024
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Name and Institution (Required)
Name: Lizzie Lundgren
Institution: Harvard University
Describe the update
This draft PR contains updates for KPP standalone interface from Obin Sturm (GMAO) contained in GEOS-ESM#9. That original PR is built off of branch geos/develop in the GEOS-Chem fork in GMAO's GitHub. That version is not mergable into the standard model so this PR will be used instead.
Tagging @obin1, @yantosca
Expected changes
I have pushed several updates to this PR:
kpp_standalone_interface.ymlconfiguration file:GeosCore/kpp_standalone_interface.ymlhas been renamed toGeosCore/kppsa_interface_mod.F90. All derived types, variables, and public-facing routines have been renamed to use the prefixKppSa_, for consistency. Derived-typeobject
Kpp_Standalone_YAMLhas new been renamed toKppSa_Statefor brevity.We have added a new derived-type object
KppSa_ActiveCellto hold theActiveCelllogical flag andActive_Cell_Namefields. This is declared with!$OMP THREADPRIVATEbecause it is updated within the main parallel loop within theDO_FULLCHEMroutine.In the
KppSa_Write_Samplesroutine (formerlyWrite_Samples), we have placed the I/O code within an!$OMP CRITICALblock. This will prevent other threads from trying to write to the file, which can cause incomplete and/or corrupted files.We have added a new function
KppSa_Check_Timeto determine if we are within the time window for archiving model state specified in the YAML file. This updates a new flagKppSa_State%SkipWriteAtThisTime, which is used to determine if we need to skip writing output on this timestep.We now print the following output at initialization:
Reference(s)
None
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